% gul: The Grand Unified BiBTeX Library

% created on Wed, May 21, 2003
% connect.bib was integrated on Sep 8/9, 2003

% contains references from:
% - Yogi's segmentation gene and theory libraries
% - John's original connect.bib without redundancy and with systematic labeling

% remerged with connect.bib july 24, 2006
% duplicate entries resolved in favor of gul.bib style, with
% some irregular exceptions in a-c (then I was consistent). --JR
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=
% Warning!! Make sure you understand how to use bibtex and how
% lab keys work before modifying this file, particulrly when to
% use {{ }}. please indent properly, also. JR, Fall 2009
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
% JR, 06/07/2010:
% I just went through this whole file and cleaned it up. Some untidy
% entries were mine, done at the last minute. However, in order for
% this database to be a useful lab resource, you need to know what you
% are doing with this file and treat it like you would laboratory
%  code. In particular, carelessness with the entry of data will
%% result in error-filled bibliographies that have to be edited by
%                  hand.
%Here are some considerations:
% ACCURACY:
% 1. For articles, ALWAYS give volume and page numbers in ASCII (don't
%                  blindly paste). Always give the full page range
%                  unless it is an article number. List an article
%                  number in the 'pages' field, do not use an
%                  'articlenumber' (or whatever) field.
% 2. For articles, NEVER give the month or issue number. If a style
%                  is used that prints these, coverage will be uneven.
% 3. For articles, NEVER use a journal abbreviation. ALWAYS put the
%                  name in full. A paper we publish will get abbrevs in
%                  production. The proper way to do abbrevs is a set of
%                  macros for a particular bst/dtx; they should NOT be
%                  in the database.
% 4. For EVERYTHING, please obey the laboratory first-author-last-name
%                  two digit date convention, with initials to remove
%                  ambiguity. The only exceptions are items with no
%                  author (see Ibm07 for an example). Certain other
%                  special cases have a duplicate entry with the
%                  correct key elsewhere.
% 5. Capitalization in titles. If you want capital letters in titles,
%                  you must use {}, as in {DNA}. If you need a capital
%                  letter in an italicized word, you need extra
%                  brackets or it won't work:  {{\em {{D}rosophila}}.
% TIDYNESS:
% 1. Indentation: Like computer code, indentation improves
%                  readability. I use emacs bibtex-fill-mode, but there
%                  are other ways. I do not insist on a fixed
%                  indentation style, but PLEASE keep lines to 80-90
%                  bytes, make sure fields are indented relative to
%                  entries (records), and make sure line breaks in
%                  fields are indented relative to the field
%                  indentifier ('author', 'title', etc.).
%
%         Mondo Thanks!!! --JR
%
% Current Revision $Revision: 1.33 $
% On branch $Name:  $
% Latest Change by $Author: reinitz $ on $Date: 2010/06/08 01:03:12 $

@Article{Aarts85,
  author       = "Aarts E. H. L. and P. J. M. van Laarhoven",
  title        = "Statistical cooling algorithm: {A} general approach to
                 combinatorial optimization problems",
  journal      = "Philips Journal of Research",
  year         = "1985",
  volume       = "40",
  pages        = "193--226",
}


@InCollection{Aarts86,
  author       = "E. H. L. Aarts and F. M. J. de Bont and E. H. A.
                 Habers and P. J. M. van Laarhoven",
  title        = "A parallel statistical cooling algorithm",
  booktitle    = "Proceedings of the Symposium on the Theoretical
                 Aspects of Computer Science",
  year         = "1986",
  volume       = "210",
  pages        = "87--97",
}

@Article{Abrahante03,
  author       = "J. E. Abrahante and A. L. Daul and M. Li and M. L.
                 Volk and J. M. Tennessen and E. A. Miller and A. E.
                 Rougvie",
  title        = "The {{\em {C}aenorhabditis elegans}} {\em
                 hunchback-like} gene {\em lin-57/hbl-1} controls
                 developmental time and is regulated by micro{RNA}s",
  journal      = "Developmental Cell",
  year         = "2003",
  volume       = "4",
  pages        = "625--637",
}
}

@Article{Abrell00,
  author       = "S. Abrell and P. Carrera and H. J{\"{a}}ckle",
  title        = "A modifier screen of ectopic {{\em {K}r{\"{u}}ppel}}
                 activity identifies autosomal {{\em {{D}rosophila}}}
                 chromosomal sites and genes required for normal eye
                 development",
  journal      = "Chromosoma",
  year         = "2000",
  volume       = "109",
  pages        = "334--342",
}

@Article{Ackers82,
  author =   {G. K. Ackers and A. D. Johnson and M. A. Shea},
  title =    {Quantitative model for gene-regulation by
                  lambda-phage repressor},
  journal =      {Proceedings of the National Academy of Sciences USA},
  year =     {1982},
  volume =   {79},
  pages =    {1129-1133}
}


@Article{Adiga00,
  author       = "P. S. Umesh Adiga and B. B. Chaudhuri",
  title        = "Segmentation and counting {FISH} signals in confocal
                 microscopy images",
  journal      = "Micron",
  year         = "2000",
  volume       = "31",
  pages        = "5--15",
}


@Article{Adiga99,
  author       = "P. S. Umesh Adiga and B. B. Chaudhuri",
  title        = "Efficient cell segmentation tool for confocal
                 microscopy tissue images and quantitative evaluation of
                 {FISH} signal",
  journal      = "Microscopy Research and Technique",
  year         = "1999",
  volume       = "44",
  pages        = "49--68",
}

@Article{Aegerter-Wilmsen05,
  author       = "T. Aegerter-Wilmsen and C. M. Aegerter and T.
  Bisseling",
  title        = "Model for the robust establishment of precise
  proportions in the early {{\em {{D}rosophila}}} embryo",
  journal      = "Journal of Theoretical Biology",
  year         = "2005",
  volume       = "234",
  pages        = "13--19",
}


@ARTICLE{Aero90,
  author       = "E. L. Aero and S. A. Vakulenko and A. D. Vilesov",
  title        = {Kinetic-theory of microphase separation in block copolymers},
  journal      ="Journal de Physique",
  volume       = "51",
  year         = "1990",
  pages        = "2205-2226",
}


@Article{Aitchison77,
  author =   {J. Aichison and J. Habbema and J. Kay},
  title =    {A Critical Comparison of Two Methods of Statistical
                   Discrimination},
  journal =      {Applied Statistics},
  year =     {1977},
  volume =   {26},
  pages =    {15-25}
}

@Book{Aizen00a,
  author    = {I. N. Aizenberg and N. N. Aizenberg and J. Vandewalle},
  title     = {Multi-valued and universal binary neurons: theory,
               learning, applications},
  publisher = {Kluwer Academic Publishers},
  address   = {Boston/Dordrecht/London},
  year      = {2000}
}

@inproceedings{Aizen00b,
   author    = {I. Aizenberg and N. Aizenberg and C. Butakov and E. Farberov},
   title     = {Image Recognition on the Neural Network based on
                  Multi-Valued Neurons},
   booktitle = {Proceedings of the 15th International Conference on
                  Pattern Recognition},
   year      = {September 3-8, 2000},
   editor    = {A. Sanfeliu et al},
   publisher = {IEEE Computer Society Press},
   volume    = {2},
   pages     = {993-996},
   address   = {Barcelona, Spain}
}

@Article{Aizen02a,
  author =   {Igor Aizenberg and Ekaterina Myasnikova and Maria
                  Samsonova and John Reinitz},
  title =    {Temporal classification of {{\em {D}rosophila}} segmentation
                  gene expression patterns by the multi-valued neural
                  recognition method},
  journal =      {Mathematical Biosciences},
  year =     {2002},
  volume =   {159},
  pages =    {145-159}
}

@InProceedings{Aizen02b,
  author =   {I. Aizenberg and C. Butakoff and E. Myasnikova and
                  M. Samsonova and J. Reinitz},
  title =    {Classification of the Images of Gene Expression
                  Patterns Using Neural Network Based on Multi-Valued
                  Neurons with the Minimal Number of Inputs},
  booktitle =    {SPIE Proceedings},
  pages =    {10-19},
  year =     {2002},
  editor =   {Nasser M. Nasrabadi and Aggelos K. Katsaggelos},
  volume =   {4668}
}

@InBook{Aizen99,
  author    = {I. N. Aizenberg and N. N. Aizenberg},
  title     = {Pattern recognition using neural network based on
                  multi-valued neurons},
  series    = {Lecture Notes in Computer Science},
  volume    = {1607-II},
  publisher = {Springer-Verlag},
  pages     = {383-392},
  year      = {1999}
}

@Book{Aizenberg00a,
  author       = "I. N. Aizenberg and N. N. Aizenberg and J.
                 Vandewalle",
  title        = "Multi-valued and universal binary neurons: theory,
                 learning, applications",
  publisher    = "Kluwer Academic Publishers",
  address      = "Boston/Dordrecht/London",
  year         = "2000",
}

@InProceedings{Aizenberg00b,
  author       = "I. Aizenberg and N. Aizenberg and C. Butakov and E.
                 Farberov",
  title        = "Image Recognition on the Neural Network based on
                 Multi-Valued Neurons",
  booktitle    = "Proceedings of the 15th International Conference on
                 Pattern Recognition",
  year         = "2000",
  editor       = "A. Sanfeliu et al.",
  publisher    = "IEEE Computer Society Press",
  volume       = "2",
  pages        = "993--996",
  address      = "Barcelona, Spain",
}

@InProceedings{Aizenberg01a,
  author =   "Igor Aizenberg and Ekaterina Myasnikova and Maria Samsonova",
  title =    " Classification of the Images of Gene Expression
          Patterns using Neural Networks Based on Multi-Valued Neurons",
  editor =   " J. Mira and  A. Prieto",
  volume =   "Part II",
  pages =    "219-226",
  booktitle =    " 6th International Work-Conference on Artificial and
          Natural Networks, IWANN 2001",
  year =     "2001",
  publisher =    "Springer-Verlag",
  address =  "Berlin Heidelberg",
  month =    "June"
}


@InProceedings{Aizenberg01b,
  author       = "I. Aizenberg and E. Myasnikova and M. Samsonova",
  title        = "Application of the Neural Networks Based on
                 Multi-Valued Neurons to Classification of the Images of
                 Gene Expression Patterns",
  booktitle    = "FUZZY DAYS in Dortmund, Germany, International
                 Conference on Computational Intelligence",
  year         = "2001",
  publisher    = "Springer",
  pages        = "291--304",
}

@Article{Aizenberg01c,
  author =   {Igor Aizenberg and Ekaterina Myasnikova and Maria
                  Samsonova and John Reinitz},
  title =    { Application of the Neural Networks Based on
                  Multi-Valued Neurons to Classification of the Images of
                  Gene Expression Patterns},
  journal =      { Lecture Notes in Computer
                  Science},
  year =     {2001},
  volume =   {2206},
  pages =    {291-303}
}


@Article{Aizenberg02a,
  author       = "I. Aizenberg and E. Myasnikova and M. Samsonova and J.
                 Reinitz",
  title        = "Temporal classification of {{\em {D}rosopila}}
                 segmentation gene expression patterns by the
                 multi-valued neural recognition method",
  journal      = "Mathematical Biosciences",
  year         = "2002",
  volume       = "176",
  pages        = "145--159",
}

@InProceedings{Aizenberg02b,
  author       = "I. Aizenberg and C. Butakoff and E. Myasnikova and M.
                 Samsonova and J. Reinitz",
  title        = "Classification of the Images of Gene Expression
                 Patterns Using Neural Network Based on Multi-Valued
                 Neurons with the Minimal Number of Inputs",
  booktitle    = "SPIE Proceedings",
  pages        = "10--19",
  year         = "2002",
  editor       = "N. M. Nasrabadi and A. K. Katsaggelos",
  volume       = "4668",
}

@InBook{Aizenberg99,
  author       = "I. N. Aizenberg and N. N. Aizenberg",
  title        = "Pattern recognition using neural network based on
                 multi-valued neurons",
  series       = "Lecture Notes in Computer Science",
  volume       = "1607-II",
  publisher    = "Springer-Verlag",
  pages        = "383--392",
  year         = "1999",
}


@article{Akam87,
   author    = {Michael Akam},
   title     = {The Molecular Basis for Metameric Pattern in the
       {{\em {D}rosophila}} Embryo},
   journal   = {Development},
   year      = 1987,
   volume    = 101,
   pages     = {1-22}
}


@Article{Albert03,
  author       = "R. Albert and H. G. Othmer",
  title        = "The topology of the regulatory interactions predicts
                 the expression pattern of the segment polarity genes in
                 {{\em {D}rosophila melanogaster}}",
  journal      = "The Journal of Theoretical Biology",
  year         = "2003",
  volume       = "223",
  pages        = "1--18",
}

@article{Alexandre03,
   author    = {C. Alexandre and J-P Vincent},
   title     = {Requirements for transcriptional repression and activation by
               {E}ngrailed in {{\em {D}rosophila}} embryos},
   journal   = {Development},
   year      = {2003},
   volume    = {130},
   pages     = {729-739}
}


@article{Allen96,
    author = "M.R. Allen  and L.A. Smith",
    title = "{Monte-Carlo} {SSA}: Detecting irregular oscillations
             in the presence of coloured noise",
    journal = "Journal of Climate",
    volume ="9",
    pages ="3373--3404",
    year = "1996"
}

@article{Alves06,
    author = "F. Alves and R. Dil{\~{a}}o",
    title = "Modeling segmental patterning in {{\em {D}rosophila}}:
    Maternal and gap genes",
    journal = "Journal of Theoretical Biology",
    volume ="241",
    pages ="342--359",
    year = "2006"
}



@Article{Andrioli02,
  author =   {L. P. M. Andrioli and V. Vasisht and E.
                  Theodosopoulou and A. Oberstein and S. Small},
  title =    {Anterior repression of a {{\em {D}rosophila}} stripe
                  enhancer requires three position-specific mechanisms},
  journal =      {Development},
  year =     {2002},
  volume =   {129},
  pages =    {4931-4940}
}

@article{Andrioli04,
  author     = {L. P. Andrioli and A. L. Oberstein and M. S. G. Corado
                and D. Yu and S. Small},
  title      = {Groucho-dependent repression by {S}loppy-paired 1 differentially
                positions anterior pair-rule stripes in the {{\em
                  {D}rosophila}} embryo},
  journal    = {Developmental Biology},
  year       = {2004},
  volume     = {276},
  pages      = {541-551}
}

@Article{Angulo03,
  author       = "J. Angulo and J. Serra",
  title        = "Automatic analysis of {DNA} microarray images using
                 mathematical morphology",
  journal      = "Bioinformatics",
  year         = "2003",
  volume       = "19",
  number       = "5",
  pages        = "553--562",
}

@Article{Aravin03,
  author       = "A. A. Aravin and M. Lagos-Quintana and A. Yalcin and
                 M. Zavolan and D. Marks and B. Snyder and T.
                 Gaasterland and J. Meyer and T. Tuschl",
  title        = "The Small {RNA} Profile during {{\em {D}rosophila
                 melanogaster}} Development",
  journal      = "Developmental Cell",
  year         = "2003",
  volume       = "5",
  pages        = "337--350",
}

@Article{Arias06,
  author       = "A. M. Arias and P. Hayward",
  title        = "Filtering transcriptional noise during development:
                  concepts and mechanisms",
  journal      = "Nature Reviews Genetics",
  year         = "2006",
  volume       = "7",
  pages        = "34--44",
}


@Article{Arkin98,
  author =   {Adam Arkin and John Ross and Harley H. MacAdams},
  title =    {Stochastic Kinetic Analysis of Developmental Pathway
                  Bifurcation in Phage $\lambda$-infected
                  {{\em {E}scherichia coli}} cells},
  journal =      {Genetics},
  year =     {1998},
  volume =   {149},
  pages =    {1633-1648}
}


@Article{Arnosti96a,
  author =   {David Arnosti and Susan Gray and Scott Barolo and Jumin
                  Zhou and Michael Levine},
  title =    {The gap protein {K}nirps mediates both quenching and
                  direct repression in the {{\em {D}rosophila}} embryo},
  journal =      {The EMBO Journal},
  year =     {1996},
  volume =   {15},
  pages =    {3659-3666}
}



@Article{Arnosti96b,
  author =   {D. N. Arnosti and S. Barolo and M. Levine and S. Small},
  title =    {The eve stripe 2 enhancer employs multiple modes of
                  transcriptional synergy},
  journal =      {Development},
  year =     {1996},
  volume =   {122},
  pages =    {205-214},
}

@article {Arnosti05,
author = {Arnosti, David N. and Kulkarni, Meghana M.},
title = {Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?},
journal = {Journal of Cellular Biochemistry},
volume = {94},
number = {5},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
issn = {1097-4644},
url = {http://dx.doi.org/10.1002/jcb.20352},
doi = {10.1002/jcb.20352},
pages = {890--898},
keywords = {enhancer, transcription, enhanceosome, Cis-regulatory element},
year = {2005}
}

@Article{Artavanis91,
  author       = "S. Artavanis-Tsakonas and P. Simpson",
  title        = "Choosing a cell fate: a view from the {\em {N}otch}
                 locus",
  journal      = "Trends in Genetics",
  volume       = "7",
  year         = "1991",
  pages        = "403--408"
}


@Article{Ashyralyiev08,
  author       = "M. Ashyraliyev and J. Jaeger and J. G. Blom",
  title        = "Parameter estimation and determinability analysis
                  applied to {{\em {D}rosophila}} gap gene circuits",
  journal      = "BMC Systems Biology",
  year         = "2008",
  volume       = "2",
  pages        = "83",
}



@Article{Ashyralyiev09,
  author =   {M. Ashyraliyev and K. Siggens and H. Janssens and
                  J. Blom and M. Akam and J. Jaeger},
  title =    {Gene Circuit Analysis of the Terminal Gap Gene {\em huckebein}},
  journal =      {{PLOS} Computational Biology},
  year =     {2009},
  volume =   {5},
  pages =    {e1000548},
}

@Article{Audibert02,
  author       = "A. Audibert and D. Weil and F. Dautry",
  title        = "In vivo kinetics of mRNA splicing and transport in mammalian cells",
  journal      = "Molecular Cell Biol.",
  volume       = "22",
  year         = "2002",
  pages        = "6706--6718"
}

@Article{Ay11,
  author       = "Ahmet Ay and David N. Arnosti",
  title        = "Mathematical modeling of gene expression: a guide for the perplexed biologist",
  journal      = "Crit Rev Biochem Mol Biol",
  volume       = "46",
  number       = "2",
  year         = "2011",
  pages        = "137--151"
}

@InCollection{Azencott92,
  author =   "R. Azencott",
  title =    "Sequential simulated annealing: Speed of convergence
                  and acceleration techniques",
  booktitle =    "Simulated Annealing: Parallelization Techniques",
  year =     "1992",
  pages =    "1",
  publisher = {Wiley and Sons},
  address   = {New York}
}

@Article{Azpiazu93,
  author       = "N. Azpiazu and M. Frasch",
  title        = "{\em tinman} and {\em bagpipe}: Two homeo box genes
                 that determine cell fates in the dorsal mesoderm of
                 {{\em {D}rosophila}}",
  journal      = "Genes and Development",
  year         = "1993",
  volume       = "7",
  pages        = "1325--1340",
}

@article{Baker87,
   author    = {N. E. Baker},
   title     = {Molecular cloning of sequences from {\em wingless},
       a segment polarity gene in {{\em {D}rosophila}}: the
       spatial distribution of a transcript in embryos},
   journal   = {The {EMBO} Journal},
   year      = {1987},
   volume    = {6},
   pages     = {1765-1774}
}


@article{Baker88,
       Author = {N. E. Baker},
        title = {Localization of Transcripts from the {{\em wingless}} gene in
                  whole {{\em {D}rosophila}} Embryos},
       journal = {Development},
       year = {1988},
       volume = {103},
       pages = {289-298},
}


@Article{Banerji81,
  author       = "J. Banerji and S. Rusconi and W. Schaffner",
  title        = "Expression of a beta-globin gene is enhanced by remote
                 {SV40} {DNA} sequences",
  journal      = "Cell",
  year         = "1981",
  volume       = "27",
  pages        = "299--308",
}


@Book{Barabasi02,
  author       = "A. L. Barabasi",
  title        = "Linked: {T}he {N}ew {S}cience of {N}etworks",
  year         = "2002",
  publisher    = "Perseus Publishing",
  address      = "Cambridge, MA",
}


@Article{Barolo02a,
  author =   {Scott Barolo and James W. Posakony},
  title =    {Three habits of highly effective signalling
                  pathways: principles of transcriptional control by
                  developmental cell signaling},
  journal =      {Genes and Development},
  year =     {2002},
  volume =   {16},
  pages =    {1167-1181}
}



@Article{Barolo02b,
  author =   {Scott Barolo and Tammie Stone and Anne G. Bang and
                  James W. Posakony},
  title =    {Default repression and {N}otch signaling: {H}airless
                  acts as an adaptor to recruit the corepressors
                  {G}roucho and d{C}t{BP} tp {S}uppressor of {H}airless},
  journal =      {Genes and Development},
  year =     {2002},
  volume =   {16},
  pages =    {1964-1976}
}



@Article{Barolo97,
  author =   {Scott Barolo and Michael Levine},
  title =    {Hairy mediates dominant repression in the {{\em
                  {D}rosophila}} embryo},
  journal =      {The EMBO Journal},
  year =     {1997},
  volume =   {16},
  pages =    {2883-2891}
}




@Article{Bartel04,
  author       = "D. P. Bartel",
  title        = "{MicroRNAs}: {G}enomics, Biogenesis, Mechanism,
                 and Function",
  journal      = "Cell",
  year         = "2004",
  volume       = "116",
  pages        = "281--297",
}




@unpublished{Bartol,
    author = {J. R. Stiles and T. M. Bartol and T. J. Sejnowski
        and M. M. Salpeter and E. E. Salpeter},
    title = {MCell: A General Computer Program for Monte
        Carlo Simulation of Subcellular Biochemical
        SIgnalling},
    note = {Manuscript in preparation, Salk Institute},
    year = {1996}
}


@article{Bateman06,
        Author = {J. R. Bateman and A. M. Lee and C. T. Wu},
        Title = {Site-specific transformation of {{\em {D}rosophila}} via phi C31
        integrase-mediated cassette exchange},
        Journal = {Genetics},
        Year = {2006},
        Volume = {173},
        Number = {2},
        Pages = {769-777},
}


@article{Baumgartner90,
   author    = {Stefan Baumgartner and Markus Noll},
   title     = {Network of Interactions Among Pair-Rule Genes
       Regulating {\em paired} Expression During Primordial
       Segmentation of {{\em {D}rosophila}}},
   journal   = {Mechanisms of Development},
   year      = {1990},
   volume    = {33},
   pages     = {1-18}
}

@Article{Becker13,
	pmid = {{24204230}},
	author = {Becker, Kolja and Balsa-Canto, Eva and Cicin-Sain, Damjan and Hoermann, Astrid and Janssens, Hilde and Banga, Julio R and Jaeger, Johannes},
	title = {{Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster.}},
	journal = {{PLoS Comput. Biol.}},
	volume = {9},
	number = {10},
	pages = {e1003281},
	year = {2013},
	doi = {10.1371/journal.pcbi.1003281},
	tags = "added, Droz"
}

@article{Becskei00,
    author    = {Becskei. A. and Serrano, L.},
    title     = {Engineering stability in gene networks by
       autoregulation},
    journal   = {Nature},
    year      = {2000},
    volume    = {405},
    pages     = {590-593}
}



@Article{Bedian88,
  author       = "V. Bedian and M. C. Summers and S. A. Kauffman",
  title        = "Changes in protein synthetic activity in early {{\em
                  {D}rosophila}} embryos mutant for the segmentation gene
                 {{\em {K}r{\"{u}}ppel}}",
  journal      = "Developmental Genetics",
  year         = "1988",
  volume       = "9",
  pages        = "699--713",
}



@article{Bejsovec93,
   author    = {A. Bejsovec and E. Wieschaus},
   title     = {Segment polarity gene interactions modulate epidermal patterning in
                {{\em {D}rosophila}} embryos},
   journal   = {Development},
   year      = {1993},
   volume    = {119},
   pages     = {501-517}
}



@InCollection{Bell88,
  author       = "G. I. Bell",
  title        = "Models of Cell Adhesion Involving Specific Binding",
  booktitle    = "Physical Basis of Cell-Cell Adhesion",
  chapter      = "10",
  year         = "1988",
  editor       = "P. Bongrand",
  publisher    = "CRC Press",
}


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	title = {Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects},
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@Article{Dresch13,
	abstract = {{A rigorous analysis of transcriptional regulation at the DNA level is crucial to the understanding of many biological systems. Mathematical modeling has offered researchers a new approach to understanding this central process. In particular, thermodynamic-based modeling represents the most biophysically informed approach aimed at connecting DNA level regulatory sequences to the expression of specific genes. The goal of this review is to give biologists a thorough description of the steps involved in building, analyzing, and implementing a thermodynamic-based model of transcriptional regulation. The data requirements for this modeling approach are described, the derivation for a specific regulatory region is shown, and the challenges and future directions for the quantitative modeling of gene regulation are discussed. (c) 2013 Elsevier B.V. All rights reserved.}},
	keywords = {{PROTEIN-DNA INTERACTIONS, FACTOR-BINDING SITES, SENSITIVITY-ANALYSIS-METHODS, QUANTIFYING GENE-EXPRESSION, EARLY DROSOPHILA EMBRYOS, SYSTEMS BIOLOGY, MOTIF DISCOVERY, CHIP-CHIP, GENOME, SEGMENTATION, Transcriptional regulation, Enhancer, Thermodynamic modeling, Parameter estimation, Sensitivity analysis}},
	author = {Dresch, Jacqueline M. and Richards, Megan and Ay, Ahmet},
	title = {{A primer on thermodynamic-based models for deciphering transcriptional regulatory logic}},
	journal = {{Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms}},
	volume = {1829},
	pages = {946-953},
	year = {2013},
	doi = {10.1016/j.bbagrm.2013.04.011},
	tags = "seq2expr"
}

@article{Dresch13a,
	Bibsource = {{DBLP, http://dblp.uni-trier.de}},
	Ee = {{http://dx.doi.org/10.1137/120887588}},
	Url = {{http://dblp.org/db/journals/siamam/siamam73.html#DreschTAC13}},
	author = {Dresch, Jacqueline M. and Thompson, Marc A. and Arnosti, David N. and Chiu, Chichia},
	title = {{Two-Layer Mathematical Modeling of Gene Expression: Incorporating DNA-Level Information and System Dynamics}},
	journal = {{SIAM J. APPL. M ATH.}},
	volume = {73},
	number = {2},
	pages = {804--826},
	year = {2013},
	tags = "seq2expr"
}

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		AUTHOR = {Li, Xiao-Yong and Thomas, Sean and Sabo, Peter and Eisen, Michael and Stamatoyannopoulos, John and Biggin, Mark},
		TITLE = {The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding},
		JOURNAL = {Genome Biology},
		VOLUME = {12},
		YEAR = {2011},
		NUMBER = {4},
		PAGES = {R34},
		URL = {http://genomebiology.com/2011/12/4/R34},
		DOI = {10.1186/gb-2011-12-4-r34},
		PubMedID = {21473766},
		ISSN = {1465-6906},
		ABSTRACT = {BACKGROUND:In Drosophila embryos, many biochemically and functionally unrelated transcription factors bind quantitatively to highly overlapping sets of genomic regions, with much of the lowest levels of binding being incidental, non-functional interactions on DNA. The primary biochemical mechanisms that drive these genome-wide occupancy patterns have yet to be established.RESULTS:Here we use data resulting from the DNaseI digestion of isolated embryo nuclei to provide a biophysical measure of the degree to which proteins can access different regions of the genome. We show that the in vivo binding patterns of 21 developmental regulators are quantitatively correlated with DNA accessibility in chromatin. Furthermore, we find that levels of factor occupancy in vivo correlate much more with the degree of chromatin accessibility than with occupancy predicted from in vitro affinity measurements using purified protein and naked DNA. Within accessible regions, however, the intrinsic affinity of the factor for DNA does play a role in determining net occupancy, with even weak affinity recognition sites contributing. Finally, we show that programmed changes in chromatin accessibility between different developmental stages correlate with quantitative alterations in factor binding.CONCLUSIONS:Based on these and other results, we propose a general mechanism to explain the widespread, overlapping DNA binding by animal transcription factors. In this view, transcription factors are expressed at sufficiently high concentrations in cells such that they can occupy their recognition sequences in highly accessible chromatin without the aid of physical cooperative interactions with other proteins, leading to highly overlapping, graded binding of unrelated factors.},
}

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3. Формула для скоринга PWM:
Genome Res. 2003 Apr;13(4):579-88. Homotypic regulatory clusters in Drosophila.
Lifanov AP, Makeev VJ, Nazina AG, Papatsenko DA.

@article{Lifanov03,
	author = {Lifanov, Alexander P. and Makeev, Vsevolod J. and Nazina, Anna G. and Papatsenko, Dmitri A.}, 
	title = {Homotypic Regulatory Clusters in Drosophila},
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	year = {2003},
	doi = {10.1101/gr.668403},
	abstract ={
Cis-regulatory modules (CRMs) are transcription regulatory DNA segments (∼1 Kb range) that control the expression of developmental genes in higher eukaryotes. We analyzed clustering of known binding motifs for transcription factors (TFs) in over 60 known CRMs from 20 Drosophila developmental genes, and we present evidence that each type of recognition motif forms significant clusters within the regulatory regions regulated by the corresponding TF. We demonstrate how a search with a single binding motif can be applied to explore gene regulatory networks and to discover coregulated genes in the genome. We also discuss the potential of the clustering method in interpreting the differential response of genes to various levels of transcriptional regulators.}, 
URL = {http://genome.cshlp.org/content/13/4/579.abstract}, 
	eprint = {http://genome.cshlp.org/content/13/4/579.full.pdf+html}, 
	journal = {Genome Research} 
}

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@PhdThesis{Louis03b,
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  year =     {2007},
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    title = {Canalization of gene expression and domain shifts in the
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@unpublished{ManuCB,
    author = {Manu and S. Surkova and A. V. Spirov and
                V. Gursky and H. Janssens and A. Kim and O. Radulescu
                and C. E.  Vanario-Alonso and D. H. Sharp and
                M. Samsonova and J. Reinitz},
    title = {Canalization of gene expression and domain shifts in the
            {{\em {D}rosophila}} blastoderm by dynamical attractors},
    note = {Manuscript in preparation},
    year = {2008}
}


@unpublished{ManuPLB,
    author = {Manu and S. Surkova and A. V. Spirov and
                V. Gursky and H. Janssens and A. Kim and O. Radulescu
                and C. E.  Vanario-Alonso and D. H. Sharp and
                M. Samsonova and J. Reinitz},
    title = {Canalization of gene expression in the
            {{\em {D}rosophila}} blastoderm by gap gene cross
            regulation},
    note = {Manuscript in preparation},
    year = {2008}
}

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@article{Papatsenko09,
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	URL = {http://nar.oxfordjournals.org/content/37/17/5665.abstract}, 
	eprint = {http://nar.oxfordjournals.org/content/37/17/5665.full.pdf+html}, 
	journal = {Nucleic Acids Research} 
}

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% $Log: gul2.bib,v $
% Revision 1.33  2010/06/08 01:03:12  reinitz
% Discovered cleanup in last entry was incomplete at beinning of alphabet; fixed.
% Also added long comment at beinnin about lab conventions.
%
% Revision 1.32  2010/06/07 23:08:08  reinitz
% Added in new stuff, including last minute additions from 10/09 promoter
% grant, whatever I added my personal copy over the winter, and some new
% things for the 9/10 promoters proposal. Also went over whole files visually
% and made format repairs, checked for syntax with emacs bibtex-checker --JR.
%
% Revision 1.29  2009/10/05 04:42:50  reinitz
% Fixed vast number of capitalization errors (maybe incomplete, searched
% on 'melanogaster'), corrected
% typos in several entries, and added warning comment at the top.
% This file should be cleaned by hand, every entry inspected.
%
% Revision 1.28  2009/10/05 03:06:19  reinitz
% {\em {D}rosophila} --> {{\em {D}rosophila}} in 13 new entries.
%
% Revision 1.27  2009/10/05 00:26:21  cmartinez
%
% Fixed capitalization of new gul2.bib entries
%
% Revision 1.26  2009/10/04 21:31:54  reinitz
% Added Yves Fomekong-Nanfack thesis, Lisa thesis (cleaned up dup),
% and Masha's AD refs.
%
% Revision 1.25  2009/10/04 17:27:19  cmartinez
% Carlos:Latest gul2.bib update for promoters09j.tex
%
% Revision 1.24  2009/10/04 16:18:28  banwise
% Updated by Ah-Ram, but need to be updated more.
%
% Revision 1.23  2009/10/04 09:34:27  cmartinez
% Carlos: added unresolved references for promoters09i.tex
%
% Revision 1.22  2009/10/03 20:22:25  reinitz
% Updated refs for grant by JR.
%
% Revision 1.21  2009/10/03 15:03:12  cmartinez
% Carlos: fixed LawrenceCE90 reference
%
% Revision 1.20  2009/10/03 14:47:27  cmartinez
% Updated gul2.bib with references for transcription grant
%
% Revision 1.19  2009/10/02 07:58:29  cmartinez
% Carlos: Added new references for Aim 4 of promoters09 grant
%
% Revision 1.18  2009/07/03 15:19:07  reinitz
% Added Carlos' 09 refs from Cmartinez.bib
%
% Revision 1.17  2009/07/02 19:56:07  reinitz
% Added keywords and log.
%


@Book{Belousov2005,
    Author    = {\CB.\C2. \C1\E5\EB\EE\F3\F1\EE\E2},
    Editor    = {},
    Publisher = {\CD\E0\F3\EA\E0, \C8\E7\E4-\E2\EE \CC\EE\F1\EA\EE\E2\F1\EA\EE\E3\EE \F3\ED\E8\E2\E5\F0\F1\E8\F2\E5\F2\E0, \CC\EE\F1\EA\E2\E0, \D0\EE\F1\F1\E8\FF},
    Title     = {\CE\F1\ED\EE\E2\FB \EE\E1\F9\E5\E9 \FD\EC\E1\F0\E8\EE\EB\EE\E3\E8\E8},
    language  = {russian},
    Year      = {2005}
}

@Book{Vapnik1974,
    Author    = {\C2. \CD. \C2\E0\EF\ED\E8\EA and \C0. \DF. \D7\E5\F0\E2\EE\ED\E5\ED\EA\E8\F1},
    Editor    = {},
    Publisher = {\CD\E0\F3\EA\E0, \CC\EE\F1\EA\E2\E0},
    Title     = {\D2\E5\EE\F0\E8\FF \F0\E0\F1\EF\EE\E7\ED\E0\E2\E0\ED\E8\FF \EE\E1\F0\E0\E7\EE\E2},
    language  = {russian},
    Year      = {1974}
}

@Book{Vapnik1979,
    Author    = {\C2. \CD. \C2\E0\EF\ED\E8\EA},
    Editor    = {},
    Publisher = {\CD\E0\F3\EA\E0, \CC\EE\F1\EA\E2\E0},
    Title     = {\C2\EE\F1\F1\F2\E0\ED\EE\E2\EB\E5\ED\E8\E5 \E7\E0\E2\E8\F1\E8\EC\EE\F1\F2\E5\E9 \EF\EE \FD\EC\EF\E8\F0\E8\F7\E5\F1\EA\E8\EC \E4\E0\ED\ED\FB\EC},
    language  = {russian},
    Year      = {1979}
}

@Book{Zaks1976,
    Author    = {\CB. \C7\E0\EA\F1},
    Editor    = {},
    Publisher = {\D1\F2\E0\F2\E8\F1\F2\E8\EA\E0, \CC\EE\F1\EA\E2\E0},
    Title     = {\D1\F2\E0\F2\E8\F1\F2\E8\F7\E5\F1\EA\EE\E5 \EE\F6\E5\ED\E8\E2\E0\ED\E8\E5},
    language  = {russian},
    Year      = {1976}
}

@Book{Sachs82,
    Author    = {Lothar Sachs},
    Publisher = {Springer},
    Address = {US},
    Title     = {Applied Statistics},
    doi = {10.1007/978-1-4684-0123-3},
    Year      = {1982}
}

@Book{Zhimulev2003,
    Author    = {\C8.\D4. \C6\E8\EC\F3\EB\E5\E2},
    Editor    = {},
    Publisher = {\D1\E8\E1\E8\F0\F1\EA\EE\E5 \F3\ED\E8\E2\E5\F0\F1\E8\F2\E5\F2\F1\EA\EE\E5 \E8\E7\E4\E0\F2\E5\EB\FC\F1\F2\E2\EE, \CD\EE\E2\EE\F1\E8\E1\E8\F0\F1\EA, \D0\EE\F1\F1\E8\FF},
    Title     = {\CE\E1\F9\E0\FF \E8 \EC\EE\EB\E5\EA\F3\EB\FF\F0\ED\E0\FF \E3\E5\ED\E5\F2\E8\EA\E0},
    language  = {russian},
    Year      = {2003}
}

@Book{Korochkin2002,
    Author    = {\CB. \C8. \CA\EE\F0\EE\F7\EA\E8\ED},
    Editor    = {},
    Publisher = {\C8\E7\E4-\E2\EE \CC\EE\F1\EA\EE\E2\F1\EA\EE\E3\EE \F3\ED\E8\E2\E5\F0\F1\E8\F2\E5\F2\E0, \CC\EE\F1\EA\E2\E0, \D0\EE\F1\F1\E8\FF},
    Title     = {\C1\E8\EE\EB\EE\E3\E8\FF \E8\ED\E4\E8\E2\E8\E4\F3\E0\EB\FC\ED\EE\E3\EE \F0\E0\E7\E2\E8\F2\E8\FF},
    language  = {russian},
    Year      = {2002}
}

@Article{Myasnikova2001,
    Author  = {\CC\FF\F1\ED\E8\EA\EE\E2\E0, \C5.  and \D1\E0\EC\F1\EE\ED\EE\E2\E0, \C0.  and \D1\E0\EC\F1\EE\ED\EE\E2\E0, \CC.  and \D0\E5\E9\ED\E8\F2\F6,\C4.},
    Journal = {\CC\EE\EB\E5\EA\F3\EB\FF\F0\ED\E0\FF \E1\E8\EE\EB\EE\E3\E8\FF},
    Title   = {\CF\F0\EE\F1\F2\F0\E0\ED\F1\F2\E2\E5\ED\ED\E0\FF \F0\E5\E3\E8\F1\F2\F0\E0\F6\E8\FF \E4\E0\ED\ED\FB\F5 \EE\E1 \FD\EA\F1\EF\F0\E5\F1\F1\E8\E8 \E3\E5\ED\EE\E2 in situ},
    Year    = {2001},
    Volume  = {35},
    language  = {russian},
    Pages   = {1110--1115}
}

@Article{Ratushniy2005,
    Author  = {\D0\E0\F2\F3\F8\ED\FB\E9 \C0. \C2. and \CB\E8\F5\EE\F8\E2\E0\E9 \C2. \C0. and \C0\ED\E0\ED\FC\EA\EE \C5. \C0. and \C2\EB\E0\E4\E8\EC\E8\F0\EE\E2 \CD. \C2. and
                \C3\F3\ED\E1\E8\ED \CA. \C2. and \CB\E0\F8\E8\ED \D1. \C0. and \CD\E5\E4\EE\F1\E5\EA\E8\ED\E0 \C5. \C0. and \CD\E8\EA\EE\EB\E0\E5\E2 \D1. \C2. and
                \CE\EC\E5\EB\FC\FF\ED\F7\F3\EA \CB. \C2. and \CC\E0\F2\F3\F8\EA\E8\ED \DE. \C3. and \CA\EE\EB\F7\E0\ED\EE\E2, \CD. \C0.},
    Journal = {\C8\ED\F4\EE\F0\EC\E0\F6\E8\EE\ED\ED\FB\E9 \C2\E5\F1\F2\ED\E8\EA \C2\CE\C3\E8\D1},
    Title   = {\CD\EE\E2\EE\F1\E8\E1\E8\F0\F1\EA\E0\FF \F8\EA\EE\EB\E0 \F1\E8\F1\F2\E5\EC\ED\EE\E9 \EA\EE\EC\EF\FC\FE\F2\E5\F0\ED\EE\E9 \E1\E8\EE\EB\EE\E3\E8\E8: \E8\F1\F2\EE\F0\E8\F7\E5\F1\EA\E8\E9 \FD\EA\F1\EA\F3\F0\F1 \E8 \EF\E5\F0\F1\EF\E5\EA\F2\E8\E2\FB \F0\E0\E7\E2\E8\F2\E8\FF},
    Year    = {2005},
    Volume  = {9},
    Number  = {2},
    language  = {russian},
    Pages   = {232--261}
}

@Article{Samsonova2006,
    Author  = {\D1\E0\EC\F1\EE\ED\EE\E2\E0, \CC.\C3. and \C3\F3\F0\F1\EA\E8\E9, \C2.\C2. and \CA\EE\E7\EB\EE\E2, \CA.\CD. and \D1\E0\EC\F1\EE\ED\EE\E2, \C0.\CC.},
    Journal = {\CD\E0\F3\F7\ED\EE-\F2\E5\F5\ED\E8\F7\E5\F1\EA\E8\E5 \E2\E5\E4\EE\EC\EE\F1\F2\E8 \D1\CF\E1\C3\D2\D3},
    Title   = {\D1\E8\F1\F2\E5\EC\ED\FB\E9 \EF\EE\E4\F5\EE\E4 \EA \E8\F1\F1\EB\E5\E4\EE\E2\E0\ED\E8\FE \EE\F0\E3\E0\ED\E8\E7\EC\EE\E2},
    Year    = {2006},
    Volume  = {2},
    language  = {russian},
    Pages   = {222--234}
}

@Book{Kolchanov2005,
    Author  = {Kolchanov and Hofest\"adt},
    Editor    = {},
    Publisher = {Springer Science+Business Media, Inc.},
    Title     = {Bioinformatics of Genome Regulation and Structure II},
    Year      = {2005}
}

@Article{Kitano2002,
    Author  = {Kitano, H.},
    Journal = {Science},
    Title   = {Systems biology: a brief overview},
    Year    = {2002},
    Volume  = {295},
    Number  = {5560},
    Pages   = {1662--1664}
}

@Article{Banerjee2002,
    Author  = {Banerjee N. and Zhang M. Q.},
    Journal = {Current Opinion Microbiology},
    Title   = {Functional genomics as applied to mapping transcription regulatory networks},
    Year    = {2002},
    Volume  = {5},
    Pages   = {313--317}
}

@Article{ShavTal2006,
    Author  = {Shav-Tal Y.},
    Journal = {Soft Matter},
    Title   = {The living test-tube: imaging of real-time gene expression},
    Year    = {2006},
    Volume  = {2},
    Pages   = {361--370}
}

@InProceedings{Kozlov2007,
  author       = "Kozlov K. and Pisarev A. and Matveeva A. and Kaandorp J. and Samsonova M.",
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  booktitle    = "Proceedings of the 4th International Symposium on Networks in Bioinformatics (ISNB)",
  year         = "2007",
  pages        = "204",
  address      = "Amsterdam, The Netherlands"
}

@Article{Mendes1998,
    Author  = {Mendes P. and Kell D. B.},
    Journal = {Bioinformatics},
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    Volume  = {14},
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@Article{Moles2003,
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    Year    = {2003},
    Volume  = {13},
    Pages   = {2467--2474}
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@Article{Maple,
    Author  = {Maple},
    language  = {russian},
    Title   = {\C0\E4\F0\E5\F1:http://www.maplesoft.com}
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@Article{Mathematica,
    Author  = {Maple},
    language  = {russian},
    Title   = {\C0\E4\F0\E5\F1:http://www.wolfram.com}
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@Article{Matlab,
    Author  = {Matlab},
    language  = {russian},
    Title   = {\C0\E4\F0\E5\F1:http://www.mathworks.com}
}

@Article{Byrd1988,
    Author  = {Byrd R. H. and Shnabel R. B. and Shultz G. A.},
    Journal = {Mathematical Programming},
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    Year    = {1988},
    Volume  = {40},
    Pages   = {247--263}
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@Book{Laarhoven1987,
    Author  = {van Laarhoven P. J. M. and Aarts E. H. L.},
    Editor    = {},
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    Title     = {Bioinformatics of Genome Regulation and Structure II},
    Year      = {1987}
}

@PhdThesis{Boese1996,
  author       = {Boese K.D.},
  title        = {Models for iterative global optimization},
  school       = {University of California at Los Angeles, Los Angeles, CA},
  year         = {1996}
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@Article{Geman1984,
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    Title   = {Stochastic Relaxation, Gibbs distributions, and Bayesian restoration of Images},
    Year    = {1984},
    Volume  = {6},
    Pages   = {721}
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@Article{Hajek1988,
    Author  = {Hajek B.},
    Journal = {Mathematics of Operations Research},
    Title   = {Cooling schedules of optimal annealing},
    Year    = {1988},
    Volume  = {13},
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@Article{Johnson1989,
    Author  = {Johnson D. S. and Aargon C. R. and McGeoch L. A. and Shevon C.},
    Journal = {Operations Research},
    Title   = {optimization by simulated annealing: an experimantal evaluation; part 1, graph partitioning},
    Year    = {1989},
    Volume  = {37},
    Pages   = {865--892}
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@Article{Ingber1992,
  author       = {Lester Ingber},
  title        = {Genetic algorithms and very fast simulated annealing - a comparison},
  journal      = {Mathematical Computer Modeling},
  year         = {1992},
  volume       = {16},
  pages        = {87--100}
}

@Book{Goldberg1989,
    Author  = {Goldberg D. E.},
    Editor    = {},
    Publisher = {Addison-Wesley Professional},
    Address   = {New York, NY},
    Title     = {Genetic Algorithms in Search, Optimization, and Machine Learning},
    Year      = {1989}
}

@InProceedings{Back1991,
  author       = {B\"ack T. and Hoffmeister F.},
  title        = {Extended Selection Mchanisms in genetic Algorithms},
  editor       = {Belew R. K. and Booker L. B.},
  booktitle    = {Proceedings of Fourth International Conference on Genetic ALgorithms (ICGA-4)},
  publisher    = {Morgan Kauffmann Publishers Inc.},
  address      = {San Mateo, CA},
  year         = {1991},
  pages        = {92--99}
}

@InProceedings{Whitley1989,
  author       = {Whitley D.},
  title        = {The genitor algorithm and selection pressure: why rank-based allocation of reproductive trials is best},
  editor       = {Schaffer J. D.},
  booktitle    = {Proceedings of Third International Conference on Genetic ALgorithms},
  publisher    = {Morgan Kauffmann Publishers Inc.},
  address      = {San Francisco, CA},
  year         = {1989},
  pages        = {116--121}
}

@InProceedings{Baker1987,
  author       = {Baker J. E.},
  title        = {The genitor algorithm and selection pressure: why rank-based allocation of reproductive trials is best},
  editor       = {Grefenstette J. J.},
  booktitle    = {Proceedings of Second International Conference on Genetic ALgorithms and their Applications},
  publisher    = {Lawrence Erlbaum  Associates},
  address      = {Hillsdale, NJ},
  year         = {1987},
  pages        = {14--21}
}

@PhdThesis{Miller1997,
  author       = {Miller B.L.},
  title        = {Noise, sampling, and efficient genetic algorithms},
  school       = {University of Illinois at Urbana-Champaign},
  address      = {Champaign, IL},
  year         = {1997}
}

@Article{Lawler1966,
  author       = {Lawler E. L. and Wood D. E.},
  title        = {Branch-and-bound methods: a survey},
  journal      = {Operations Research},
  year         = {1966},
  volume       = {14},
  pages        = {699--719}
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@Article{Mitten1970,
  author       = {Mitten L. G.},
  title        = {Branch-and-bound methods: general formulation and properties},
  journal      = {Operations Research},
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  volume       = {18},
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@Book{Koza1999,
    Author  = {Koza J. R. and Andre D. and Benett F. H. and Keane M. A.},
    Editor    = {},
    publisher = {Morgan Kauffmann Publishers Inc.},
    address   = {San Francisco, CA},
    Title     = {Genetic programming III: Darwanian Invention \& Problem Solving},
    Year      = {1999}
}

@Article{Forrest1993,
  author       = {Forrest S.},
  title        = {Genetic algorithms: principles of natural selection applied to computation},
  journal      = {Science},
  year         = {1993},
  volume       = {261},
  pages        = {872--878}
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@Article{Runarsson2000,
  author       = {Runarsson T. P. and Yao X.},
  title        = {Stochastic ranking for constrained evolutionary optimization},
  journal      = {IEEE Transactions on Evolutionary Computation},
  year         = {2000},
  volume       = {4},
  pages        = {284--294}
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@Article{Zi2006,
  author       = {Zi Z. and Klipp E.},
  title        = {SBML-PET: a systems biology markup language based parameter estimation tool},
  journal      = {Bioinformatics},
  year         = {2006},
  volume       = {22},
  pages        = {2704--2705}
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@Article{Hooke1961,
  author       = {Hooke R. and Jeeves T. A.},
  title        = {Direct solution of numerical and statistical problems},
  journal      = {Journal Of The Association For Computing Machinery},
  year         = {1961},
  volume       = {8},
  pages        = {212--229}
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@InProceedings{Wright1995,
  author       = {Wright M. H.},
  title        = {Direct search methods: once scorned, now respectable},
  editor       = {Griffiths D. F. and Watson G. A.},
  booktitle    = {Proceedings of the 1995 Bienanial Dundee Conference on Numerical Analysis},
  publisher    = {Addison Wesley Longman},
  address      = {Harlow, UK},
  year         = {1995},
  pages        = {191--208}
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@Article{Powell1998,
  author       = {Powell M. J. D.},
  title        = {Direct search algorithms for optimization calculations},
  journal      = {Acta numerica},
  year         = {1998},
  volume       = {7},
  pages        = {287--336}
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@Article{Kolda2003,
  author       = {Kolda T. G. and Lewis R. M. and Torczon V.},
  title        = {Optimization of direct search: new perspectives on some classical and modern methods},
  journal      = {SIAM Review},
  year         = {2003},
  volume       = {45},
  pages        = {385--482}
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@Article{Nelder1965,
  author       = {Nelder J. A. and Mead R.},
  title        = {A simplex method for function minimization},
  journal      = {Computer Journal},
  year         = {1965},
  volume       = {7},
  pages        = {308--313}
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@Article{Torczon1997,
  author       = {Torczon V.},
  title        = {On the convergence of pattern search algorithms},
  journal      = {SIAM Journal on Optimization},
  year         = {1997},
  volume       = {7},
  pages        = {1--25}
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@Article{Lagarias1998,
  author       = {Lagarias J. C. and Reeds J. A. and Wright M. H. Wright P. E.},
  title        = {Convergence properties of the Nelder-Mead simplex method in low dimensions},
  journal      = {SIAM Journal on Optimization},
  year         = {1998},
  volume       = {9},
  pages        = {112--147}
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@Article{Adifor,
    Author  = {Adifor},
    language  = {russian},
    Title   = {\C0\E4\F0\E5\F1:http://www-unix.mcs-anl.gov/autodiff/ADIFOR}
}

@Article{Ampl,
    Author  = {Ampl},
    language  = {russian},
    Title   = {\C0\E4\F0\E5\F1:http://www.ampl.com}
}

@Article{Gams,
    Author  = {Gams},
    language  = {russian},
    Title   = {\C0\E4\F0\E5\F1:http://www.gams.com}
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@Book{Noccedal1999,
    Author  = {Noccedal J. and Wright S. J.},
    Editor    = {},
    publisher = {Springer},
    address   = {New York, NY},
    Title     = {Numerical Optimization},
    Year      = {1999}
}

@Book{Conn2000,
    Author  = {Conn A. R. and Gould I. M. and Toint P. L.},
    Editor    = {},
    publisher = {Number 1 in MPS-SIAM Series on Optimization, SIAM},
    address   = {Philadelphia, PA},
    Title     = {Trust-Region Methods},
    Year      = {2000}
}

@Article{Marquardt1963,
  author       = {Marquardt D. W.},
  title        = {An algorithm  for least-squares estimation of nonlinear parameters},
  journal      = {SIAM Journal on Applied Mathematics},
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  pages        = {431--441}
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@TechReport{Bus1975,
  author       = {Bus J. C. P. and van Domselaar B. and Kok J.},
  title        = {Nonlinear Least Squares Estimation},
  institution  = {Stichting Mathematisch Centrum, Amsterdam},
  year         = {1975},
  number       = {NW 17/75}
}

@Booklet{Madsen2004,
    Author  = {Madsen K and Nielsen H. B. and Tingleff O.},
    Editor    = {},
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    Title     = {Methods for Non-Linear Least Squares Problems},
    Year      = {2004}
}

@Article{McKinnon1998,
  author       = {McKinnon K. I. M.},
  title        = {Convergence properties of the Nelder-Mead simplex method to a nonstationary point},
  journal      = {SIAM Journal on Optimization},
  year         = {1998},
  volume       = {9},
  pages        = {148--158}
}

@Article{Timmer1998,
  author       = {Timmer J.},
  title        = {Modeling noisy time series: physiological tremor},
  journal      = {International Journal of Bifurcation and Chaos},
  year         = {1998},
  volume       = {8},
  pages        = {1505--1516}
}

@InProceedings{Katare2004a,
  author       = {Katare S. and Kalos A. and West D.},
  title        = {A hybrid swarm optimizer for efficient parameter estimation},
  editor       = {Greenwood G. W.},
  booktitle    = {Proceedings of the 2004 IEEE Congress on Evolutionary Computation},
  publisher    = {IEEE Press},
  address      = {Portland, OR},
  year         = {1995},
  month        = {June},
  pages        = {309--315}
}

@Article{Katare2004b,
  author       = {Katare S. and Bhan A. and Caruthers J. M. and Delgass W. N. and Venkatasubramanian V.},
  title        = {A hybrid genetic algorithm for parameter estimation of large kinetic models},
  journal      = {Computers and Chemical Engineering},
  year         = {2004},
  volume       = {28},
  pages        = {2569--2581}
}

@InProceedings{Kennedy1998,
  author       = {Kennedy J.},
  title        = {The behavior of particles},
  editor       = {Porto V. W. and Saravanan N. and Waagen D. and Eiben A. E.},
  booktitle    = {EP'98: Proceedings of the 7th International Conference on Evolutionary Programming VII},
  publisher    = {Springer-Verlag},
  address      = {London, UK},
  year         = {1998},
  pages        = {581--589}
}

@Book{Kennedy2001,
    Author  = {Kennedy J. and Eberhart R. C.},
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    publisher = {Morgan Kauffmann Publishers Inc.},
    address   = {San Francisco, CA},
    Title     = {Swarm Intelligence},
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@Article{Laguna2005,
  author       = {Laguna M. and Marti R.},
  title        = {Experimental testing of advanced scatter search design for global optimization of multimodal functions},
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  volume       = {33},
  pages        = {235--255}
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@Article{Rodriguez2006,
  author       = {Rodriguez-Fernandez M. and Egea J. A. and Banga J. R.},
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@Article{Egea2007,
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@Article{Ashyralyiev2009a,
  author =   {Maksat Ashyraliyev and Yves Fomekong-Nanfack and Jaap A. Kaandorp and Joke G. Blom},
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@Article{Hamacher2006,
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@Article{Mancera2004,
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@Techreport{Groenen1991,
    Author      = {Patrick Groenen and Willem J. Heiser},
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@Techreport{Voudouris1994,
    Author  = {Chris Voudouris and Edward Tsang},
    Title   = {The Tunneling Algorithm for Partial CSPs and Combinatorial Optimization problems},
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@article{Levy1985,
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@Article{Liu2003,
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@Book{Petukhov82,
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@Article{Ioffe52,
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@article{Gonsales05,
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  author={\C3\EE\ED\F1\E0\EB\E5\F1, \D0. and \C2\F3\E4\F1, \D0.},
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@MISC{Fowlkes08,
    author = {Charless C. Fowlkes and Cris L. Luengo Hendriks and Soile V. E. Ker\:anen and Gunther H. Weber and Oliver R\:ubel and Min-yu Huang and Sohail Chatoor and Angela H. Depace and Lisa Simirenko and Amy Beaton and Richard Weiszmann and Susan Celniker and Bernd Hamann and David W and Mark D. Biggin and Michael B. Eisen and Jitendra Malik},
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@article{Little11,
    author = {Shawn C. Little and Gasper Tka\^cik and Thomas B. Kneeland and Eric F. Wieschaus and Thomas Gregor},
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@ARTICLE{Gutenkunst07,
  author =       {Gutenkunst RN and Waterfall and Casey FP and Brown KS and Myers CR and Sethna JP},
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  number =       {10},
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@ARTICLE{Saccomani10,
  author =       {Maria Pia Saccomani},
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  year =         {2010},
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@ARTICLE{Pohjanpalo78,
  author =       {Pohjanpalo, H.},
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@ARTICLE{Evans00,
  author =       {Evans N.D. and Chappell M.J.},
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@ARTICLE{Stigter07,
  author =       {Stigter J.D. and Peeters R.L.M.},
  title =        {On a Geometric Approach to the Structural Identifiability Problem
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@ARTICLE{Evans02,
  author =       {Evans N.D. and Chapman  M.J. and Chappell  M.J. and Godfreya K.R.},
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@ARTICLE{Ashyraliyev08,
  author =       {Maksat Ashyraliyev and Johannes Jaeger and Joke G. Blom},
  title =        {On Parameter Estimation and Determinability for Drosophila Gap Gene Circuits},
  journal =      {BMC Systems Biology},
  year =         {2008},
  volume =       {2},
  number =       {83},
  note =         {doi:10.1186/1752-0509-2-83}
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@ARTICLE{Hengl07,
  author =       {S. Hengl and C. Kreutz and J. Timmer and T. Maiwald},
  title =        {Data-based identifiability analysis of non-linear dynamical models},
  journal =      {Bioinformatics},
  year =         {2007},
  volume =       {23},
  pages =        {2612--2618}
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@ARTICLE{Raue09,
  author =       {A. Raue and C. Kreutz and T. Maiwald and J. Bachmann and M. Schilling and U. Klingmuller and J. Timmer},
  title =        {Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood},
  journal =      {Bioinformatics},
  year =         {2009},
  volume =       {25},
  pages =        {1923--1929}
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 # "\providecommand{\singleletter}[1]{#1}%"
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@String{advp = {Adv. Phys.}}
@String{anndp = {Ann. d. Physik}}
@String{eurjp = {Eur. J. Phys.}}
@String{jcam = {J. Comput. Appl. Math.}}
@String{jchemp = {J. Chem. Phys.}}
@String{intjtd = {Int. J. Thermodyn.}}
@String{jmbio = {J. Math. Biol.}}
@String{jmphys = {J. Math. Phys.}}
@String{jpa = {J. Phys. A}}
@String{jpcs = {J. Phys.: Conference Series}}
@String{jps = {J. Phys. Studies}}
@String{jstatp = {J. Stat. Phys.}}
@String{physa = {Physica A}}
@String{prep = {Phys. Rep.}}
@String{preva = {Phys. Rev. A}}
@String{prevb = {Phys. Rev. B}}
@String{preve = {Phys. Rev. E}}
@String{prevl = {Phys. Rev. Lett.}}
@String{plms = {Proc. London Math. Soc.}}
@String{pnas = {Proc. Natl. Acad. Sci. USA}}
@String{reppp = {Rep. Prog. Phys.}}
@String{revmp = {Rev. Mod. Phys.}}
@String{tp = {Tech. Phys.}}
@String{zeitp = {Z. Physik}}

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}

@Article{MendezCasasVazquez08,
  author = 	 {M{\'e}ndez, V. and Casas-{V}{\'a}zquez, J.},
  title = 	 {Hyperbolic Reaction-Diffusion Model for Virus Infections},
  journal = 	 intjtd,
  year = 	 2008,
  volume =	 11,
  pages =	 {35--38},
}

@Article{MetzlerKlafter00,
  author = 	 {Metzler, R. and Klafter, J.},
  title = 	 {The Random Walk's Guide to Anomalous Diffusion: a Fractional Dynamics Approach},
  journal = 	 prep,
  year = 	 2000,
  volume =	 339,
  pages =	 {1--77},
}

@Article{MetzlerKlafter04,
  author = 	 {Metzler, R. and Klafter, J.},
  title = 	 {The restaurant at the end of the random walk: recent developments in the description of anomalous transport by fractional dynamics},
  journal = 	 jpa,
  year = 	 2004,
  volume =	 37,
  pages =	 {{R}161--{R}208},
}

@Book{MoninYaglom71,
  author =	 {Monin, A. S. and Yaglom, A. M.},
  title = 	 {Statistical Fluid Mechanics: Mechanics of Turbulence},
  publisher = 	 {MIT Press},
  year = 	 1971,
  volume =	 1,
  address =	 {Cambridge},
}

@Article{MontrollScher73,
  author = 	 {Montroll, E. W. and Scher, H.},
  title = 	 {Random Walks on Lattices. {IV}. {C}ontinuous-Time Walks and Influence of Absorbing Boundaries},
  journal = 	 jstatp,
  year = 	 1973,
  volume =	 9,
  pages =	 {101--135},
}

@InCollection{MontrollShlesinger84,
  author = 	 {Montroll, E. W. and Shlesinger, M. F.},
  title = 	 {On the wonderful world of random walks},
  booktitle = 	 {Nonequilibrium Phenomena {II}: {F}rom Stochastics to Hydrodynamics},
  pages =	 {1--121},
  publisher =	 {North-Holland},
  year =	 1984,
  editor =	 {Lebowitz, J. L. and Montroll, E. W.},
  volume =	 11,
  series =	 {Studies in Statistical Mechanics},
  address =	 {Amsterdam},
}

@Article{MontrollWeiss65,
  author = 	 {Montroll, E. W. and Weiss, G. H.},
  title = 	 {Random Walks on Lattices. {II}},
  journal = 	 jmphys,
  year = 	 1965,
  volume =	 6,
  pages =	 {167--181},
}

@Book{MorseFeshbach53v1,
  author =	 {Morse, Ph. M. and Feshbach, H.},
  title = 	 {Methods of Theoretical Physics},
  publisher = 	 {McGraw Hill},
  year = 	 1953,
  volume =	 1,
  address =	 {New York},
}

@Book{NIST10,
  editor =	 {Olver, F. {W.~J.} and Lozier, D. W. and Boisvert, R. F. and Clark, Ch. W.},
  title =        {{NIST} Handbook of Mathematical Functions},
  publisher =    {Cambridge University Press},
  year =         2010,
  address =      {Cambridge},
 }

@Article{OthmerEtAl88,
  author = 	 {Othmer, H. G. and Dunbar, S. R. and Alt, W.},
  title = 	 {Models of dispersal in biological systems},
  journal = 	 jmbio,
  year = 	 1988,
  volume =	 26,
  pages =	 {263--298},
}

@Book{Polyanin02,
  author =	 {Polyanin, A. D.},
  title = 	 {Handbook of Linear Partial Differential Equations for Engineers and Scientists},
  publisher = 	 {Chapman \& Hall/CRC},
  year = 	 2002,
  address =	 {Boca Raton},
}

@Article{PorraEtAl97,
  author = 	 {Porr{\`a}, J. M. and Masoliver, J. and Weiss,  G. H.},
  title = 	 {When the telegrapher's equation furnishes a better approximation to the transport equation than the diffusion approximation},
  journal = 	 preve,
  year = 	 1997,
  volume =	 55,
  pages =	 {7771--7774},
}

@Article{ScalasEtAl04,
  author = 	 {Scalas, E. and Gorenflo, R. and Mainardi, F.},
  title = 	 {Uncoupled continuous-time random walks: {S}olution and limiting behavior of the master equation},
  journal = 	 preve,
  year = 	 2004,
  volume =	 69,
  pages =	 {011107 (8~pp)},
}

@Article{Scalas06,
  author = 	 {Scalas, E.},
  title = 	 {The application of continuous-time random walks in finance and economics},
  journal = 	 physa,
  year = 	 2006,
  volume =	 362,
  pages =	 {225--239},
}

@Article{ScherLax73,
  author = 	 {Scher, H. and Lax, M.},
  title = 	 {Stochastic Transport in a Disordered Solid. {I}. {T}heory},
  journal = 	 prevb,
  year = 	 1973,
  volume =	 7,
  pages =	 {4491--4502},
}

@Article{Taylor22,
  author = 	 {Taylor, G. I.},
  title = 	 {Diffusion by Continuous Movements},
  journal = 	 plms,
  year = 	 1922,
  volume =	 20,
  pages =	 {196--212},
}

@Article{UchaikinSaenko00,
  author = 	 {Uchaikin, V. V. and Saenko, V. V.},
  title = 	 {Telegraph equation in random walk problem},
  journal = 	 jps,
  year = 	 2000,
  volume =	 4,
  pages =	 {371--379},
}

@Article{UchaikinSaenko01,
  author = 	 {Uchaikin, V. V. and Saenko, V. V.},
  title = 	 {On the theory of classic mesodiffusion},
  journal = 	 tp,
  year = 	 2001,
  volume =	 46,
  pages =	 {139--146},
}

@Book{Weiss94,
  author =	 {Weiss, G. H.},
  title = 	 {Aspects and Applications of the Random Walk},
  publisher = 	 {North--Holland},
  year = 	 1994,
  address =	 {Amsterdam},
}

@Article{Weiss02,
  author = 	 {Weiss, G. H.},
  title = 	 {Some applications of persistent random walks and the telegrapher's equation},
  journal = 	 physa,
  year = 	 2002,
  volume =	 311,
  pages =	 {381--410},
}

@Article{YusteEtAl10,
  author = 	 {Yuste, S. B. and Abad, E. and Lindenberg, K.},
  title = 	 {Reaction-subdiffusion model of morphogen gradient formation},
  journal = 	 preve,
  year = 	 2010,
  volume =	 82,
  pages =	 {061123 (9~pp)},
}

@Article{Zaslavsky02,
  author = 	 {Zaslavsky, G. M.},
  title = 	 {Chaos, fractional kinetics, and anomalous transport},
  journal = 	 prep,
  year = 	 2002,
  volume =	 371,
  pages =	 {461--580},
}

@Article{ZumofenKlafter93,
  author = 	 {Zumofen, G. and Klafter, J.},
  title = 	 {Scale-invariant motion in intermittent chaotic systems},
  journal = 	 preve,
  year = 	 1993,
  volume =	 47,
  pages =	 {851--863},
}

@Article{Schroeder11,
  author = 	 {Mark D. Schroeder and Christina Greer and Ulrike Gaul},
  title = 	 {How to make stripes: deciphering the transition from
  nonperiodic to periodic patterns in Drosophila segmentation},
  journal = 	{Development},
  year = 	 {2011},
  volume =	 {138},
  pages =	 {3067--3078}
}

@Article{Choe06,
  author = 	 {Chong Pyo Choe and Sherry C. Miller and Susan J. Brown},
  title = 	 {A pair--rule gene circuit defines
segments sequentially in the shortgerm insect Tribolium castaneum},
  journal = 	{PNAS},
  year = 	 {2006},
  volume =	 {103},
  pages =	 {6560--6564}
}

% gul: The Grand Unified BiBTeX Library

% created on Wed, May 21, 2003
% connect.bib was integrated on Sep 8/9, 2003

% contains references from:
% - Yogi's segmentation gene and theory libraries
% - John's original connect.bib without redundancy and with systematic labeling

% remerged with connect.bib july 24, 2006
% duplicate entries resolved in favor of gul.bib style, with
% some irregular exceptions in a-c (then I was consistent). --JR
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=
% Warning!! Make sure you understand how to use bibtex and how
% lab keys work before modifying this file, particulrly when to
% use {{ }}. please indent properly, also. JR, Fall 2009
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
% JR, 06/07/2010:
% I just went through this whole file and cleaned it up. Some untidy
% entries were mine, done at the last minute. However, in order for
% this database to be a useful lab resource, you need to know what you
% are doing with this file and treat it like you would laboratory
%  code. In particular, carelessness with the entry of data will
%% result in error-filled bibliographies that have to be edited by
%                  hand.
%Here are some considerations:
% ACCURACY:
% 1. For articles, ALWAYS give volume and page numbers in ASCII (don't
%                  blindly paste). Always give the full page range
%                  unless it is an article number. List an article
%                  number in the 'pages' field, do not use an
%                  'articlenumber' (or whatever) field.
% 2. For articles, NEVER give the month or issue number. If a style
%                  is used that prints these, coverage will be uneven.
% 3. For articles, NEVER use a journal abbreviation. ALWAYS put the
%                  name in full. A paper we publish will get abbrevs in
%                  production. The proper way to do abbrevs is a set of
%                  macros for a particular bst/dtx; they should NOT be
%                  in the database.
% 4. For EVERYTHING, please obey the laboratory first-author-last-name
%                  two digit date convention, with initials to remove
%                  ambiguity. The only exceptions are items with no
%                  author (see Ibm07 for an example). Certain other
%                  special cases have a duplicate entry with the
%                  correct key elsewhere.
% 5. Capitalization in titles. If you want capital letters in titles,
%                  you must use {}, as in {DNA}. If you need a capital
%                  letter in an italicized word, you need extra
%                  brackets or it won't work:  {{\em {{D}rosophila}}.
% TIDYNESS:
% 1. Indentation: Like computer code, indentation improves
%                  readability. I use emacs bibtex-fill-mode, but there
%                  are other ways. I do not insist on a fixed
%                  indentation style, but PLEASE keep lines to 80-90
%                  bytes, make sure fields are indented relative to
%                  entries (records), and make sure line breaks in
%                  fields are indented relative to the field
%                  indentifier ('author', 'title', etc.).
%
%         Mondo Thanks!!! --JR
%
% Current Revision $Revision: 1.34 $
% On branch $Name:  $
% Latest Change by $Author: reinitz $ on $Date: 2010/06/09 17:23:49 $

@Article{Aarts85,
  author       = "Aarts E. H. L. and P. J. M. van Laarhoven",
  title        = "Statistical cooling algorithm: {A} general approach to
                 combinatorial optimization problems",
  journal      = "Philips Journal of Research",
  year         = "1985",
  volume       = "40",
  pages        = "193--226",
}


@InCollection{Aarts86,
  author       = "E. H. L. Aarts and F. M. J. de Bont and E. H. A.
                 Habers and P. J. M. van Laarhoven",
  title        = "A parallel statistical cooling algorithm",
  booktitle    = "Proceedings of the Symposium on the Theoretical
                 Aspects of Computer Science",
  year         = "1986",
  volume       = "210",
  pages        = "87--97",
}

@Article{Abrahante03,
  author       = "J. E. Abrahante and A. L. Daul and M. Li and M. L.
                 Volk and J. M. Tennessen and E. A. Miller and A. E.
                 Rougvie",
  title        = "The {{\em {C}aenorhabditis elegans}} {\em
                 hunchback-like} gene {\em lin-57/hbl-1} controls
                 developmental time and is regulated by micro{RNA}s",
  journal      = "Developmental Cell",
  year         = "2003",
  volume       = "4",
  pages        = "625--637",
}
}

@Article{Abrell00,
  author       = "S. Abrell and P. Carrera and H. J{\"{a}}ckle",
  title        = "A modifier screen of ectopic {{\em {K}r{\"{u}}ppel}}
                 activity identifies autosomal {{\em {{D}rosophila}}}
                 chromosomal sites and genes required for normal eye
                 development",
  journal      = "Chromosoma",
  year         = "2000",
  volume       = "109",
  pages        = "334--342",
}

@Article{Ackers82,
  author =   {G. K. Ackers and A. D. Johnson and M. A. Shea},
  title =    {Quantitative model for gene-regulation by
                  lambda-phage repressor},
  journal =      {Proceedings of the National Academy of Sciences USA},
  year =     {1982},
  volume =   {79},
  pages =    {1129-1133}
}


@Article{Adiga00,
  author       = "P. S. Umesh Adiga and B. B. Chaudhuri",
  title        = "Segmentation and counting {FISH} signals in confocal
                 microscopy images",
  journal      = "Micron",
  year         = "2000",
  volume       = "31",
  pages        = "5--15",
}


@Article{Adiga99,
  author       = "P. S. Umesh Adiga and B. B. Chaudhuri",
  title        = "Efficient cell segmentation tool for confocal
                 microscopy tissue images and quantitative evaluation of
                 {FISH} signal",
  journal      = "Microscopy Research and Technique",
  year         = "1999",
  volume       = "44",
  pages        = "49--68",
}

@Article{Aegerter-Wilmsen05,
  author       = "T. Aegerter-Wilmsen and C. M. Aegerter and T.
  Bisseling",
  title        = "Model for the robust establishment of precise
  proportions in the early {{\em {{D}rosophila}}} embryo",
  journal      = "Journal of Theoretical Biology",
  year         = "2005",
  volume       = "234",
  pages        = "13--19",
}


@ARTICLE{Aero90,
  author       = "E. L. Aero and S. A. Vakulenko and A. D. Vilesov",
  title        = {Kinetic-theory of microphase separation in block copolymers},
  journal      ="Journal de Physique",
  volume       = "51",
  year         = "1990",
  pages        = "2205-2226",
}


@Article{Aitchison77,
  author =   {J. Aichison and J. Habbema and J. Kay},
  title =    {A Critical Comparison of Two Methods of Statistical
                   Discrimination},
  journal =      {Applied Statistics},
  year =     {1977},
  volume =   {26},
  pages =    {15-25}
}

@Book{Aizen00a,
  author    = {I. N. Aizenberg and N. N. Aizenberg and J. Vandewalle},
  title     = {Multi-valued and universal binary neurons: theory,
               learning, applications},
  publisher = {Kluwer Academic Publishers},
  address   = {Boston/Dordrecht/London},
  year      = {2000}
}

@inproceedings{Aizen00b,
   author    = {I. Aizenberg and N. Aizenberg and C. Butakov and E. Farberov},
   title     = {Image Recognition on the Neural Network based on
                  Multi-Valued Neurons},
   booktitle = {Proceedings of the 15th International Conference on
                  Pattern Recognition},
   year      = {September 3-8, 2000},
   editor    = {A. Sanfeliu et al},
   publisher = {IEEE Computer Society Press},
   volume    = {2},
   pages     = {993-996},
   address   = {Barcelona, Spain}
}

@Article{Aizen02a,
  author =   {Igor Aizenberg and Ekaterina Myasnikova and Maria
                  Samsonova and John Reinitz},
  title =    {Temporal classification of {{\em {D}rosophila}} segmentation
                  gene expression patterns by the multi-valued neural
                  recognition method},
  journal =      {Mathematical Biosciences},
  year =     {2002},
  volume =   {159},
  pages =    {145-159}
}

@InProceedings{Aizen02b,
  author =   {I. Aizenberg and C. Butakoff and E. Myasnikova and
                  M. Samsonova and J. Reinitz},
  title =    {Classification of the Images of Gene Expression
                  Patterns Using Neural Network Based on Multi-Valued
                  Neurons with the Minimal Number of Inputs},
  booktitle =    {SPIE Proceedings},
  pages =    {10-19},
  year =     {2002},
  editor =   {Nasser M. Nasrabadi and Aggelos K. Katsaggelos},
  volume =   {4668}
}

@InBook{Aizen99,
  author    = {I. N. Aizenberg and N. N. Aizenberg},
  title     = {Pattern recognition using neural network based on
                  multi-valued neurons},
  series    = {Lecture Notes in Computer Science},
  volume    = {1607-II},
  publisher = {Springer-Verlag},
  pages     = {383-392},
  year      = {1999}
}

@Book{Aizenberg00a,
  author       = "I. N. Aizenberg and N. N. Aizenberg and J.
                 Vandewalle",
  title        = "Multi-valued and universal binary neurons: theory,
                 learning, applications",
  publisher    = "Kluwer Academic Publishers",
  address      = "Boston/Dordrecht/London",
  year         = "2000",
}

@InProceedings{Aizenberg00b,
  author       = "I. Aizenberg and N. Aizenberg and C. Butakov and E.
                 Farberov",
  title        = "Image Recognition on the Neural Network based on
                 Multi-Valued Neurons",
  booktitle    = "Proceedings of the 15th International Conference on
                 Pattern Recognition",
  year         = "2000",
  editor       = "A. Sanfeliu et al.",
  publisher    = "IEEE Computer Society Press",
  volume       = "2",
  pages        = "993--996",
  address      = "Barcelona, Spain",
}

@InProceedings{Aizenberg01a,
  author =   "Igor Aizenberg and Ekaterina Myasnikova and Maria Samsonova",
  title =    " Classification of the Images of Gene Expression
          Patterns using Neural Networks Based on Multi-Valued Neurons",
  editor =   " J. Mira and  A. Prieto",
  volume =   "Part II",
  pages =    "219-226",
  booktitle =    " 6th International Work-Conference on Artificial and
          Natural Networks, IWANN 2001",
  year =     "2001",
  publisher =    "Springer-Verlag",
  address =  "Berlin Heidelberg",
  month =    "June"
}


@InProceedings{Aizenberg01b,
  author       = "I. Aizenberg and E. Myasnikova and M. Samsonova",
  title        = "Application of the Neural Networks Based on
                 Multi-Valued Neurons to Classification of the Images of
                 Gene Expression Patterns",
  booktitle    = "FUZZY DAYS in Dortmund, Germany, International
                 Conference on Computational Intelligence",
  year         = "2001",
  publisher    = "Springer",
  pages        = "291--304",
}

@Article{Aizenberg01c,
  author =   {Igor Aizenberg and Ekaterina Myasnikova and Maria
                  Samsonova and John Reinitz},
  title =    { Application of the Neural Networks Based on
                  Multi-Valued Neurons to Classification of the Images of
                  Gene Expression Patterns},
  journal =      { Lecture Notes in Computer
                  Science},
  year =     {2001},
  volume =   {2206},
  pages =    {291-303}
}


@Article{Aizenberg02a,
  author       = "I. Aizenberg and E. Myasnikova and M. Samsonova and J.
                 Reinitz",
  title        = "Temporal classification of {{\em {D}rosopila}}
                 segmentation gene expression patterns by the
                 multi-valued neural recognition method",
  journal      = "Mathematical Biosciences",
  year         = "2002",
  volume       = "176",
  pages        = "145--159",
}

@InProceedings{Aizenberg02b,
  author       = "I. Aizenberg and C. Butakoff and E. Myasnikova and M.
                 Samsonova and J. Reinitz",
  title        = "Classification of the Images of Gene Expression
                 Patterns Using Neural Network Based on Multi-Valued
                 Neurons with the Minimal Number of Inputs",
  booktitle    = "SPIE Proceedings",
  pages        = "10--19",
  year         = "2002",
  editor       = "N. M. Nasrabadi and A. K. Katsaggelos",
  volume       = "4668",
}

@InBook{Aizenberg99,
  author       = "I. N. Aizenberg and N. N. Aizenberg",
  title        = "Pattern recognition using neural network based on
                 multi-valued neurons",
  series       = "Lecture Notes in Computer Science",
  volume       = "1607-II",
  publisher    = "Springer-Verlag",
  pages        = "383--392",
  year         = "1999",
}


@Article{Albert03,
  author       = "R. Albert and H. G. Othmer",
  title        = "The topology of the regulatory interactions predicts
                 the expression pattern of the segment polarity genes in
                 {{\em {D}rosophila melanogaster}}",
  journal      = "The Journal of Theoretical Biology",
  year         = "2003",
  volume       = "223",
  pages        = "1--18",
}

@article{Alexandre03,
   author    = {C. Alexandre and J-P Vincent},
   title     = {Requirements for transcriptional repression and activation by
               {E}ngrailed in {{\em {D}rosophila}} embryos},
   journal   = {Development},
   year      = {2003},
   volume    = {130},
   pages     = {729-739}
}


@article{Allen96,
    author = "M.R. Allen  and L.A. Smith",
    title = "{Monte-Carlo} {SSA}: Detecting irregular oscillations
             in the presence of coloured noise",
    journal = "Journal of Climate",
    volume ="9",
    pages ="3373--3404",
    year = "1996"
}

@article{Alves06,
    author = "F. Alves and R. Dil{\~{a}}o",
    title = "Modeling segmental patterning in {{\em {D}rosophila}}:
    Maternal and gap genes",
    journal = "Journal of Theoretical Biology",
    volume ="241",
    pages ="342--359",
    year = "2006"
}



@Article{Andrioli02,
  author =   {L. P. M. Andrioli and V. Vasisht and E.
                  Theodosopoulou and A. Oberstein and S. Small},
  title =    {Anterior repression of a {{\em {D}rosophila}} stripe
                  enhancer requires three position-specific mechanisms},
  journal =      {Development},
  year =     {2002},
  volume =   {129},
  pages =    {4931-4940}
}

@article{Andrioli04,
  author     = {L. P. Andrioli and A. L. Oberstein and M. S. G. Corado
                and D. Yu and S. Small},
  title      = {Groucho-dependent repression by {S}loppy-paired 1 differentially
                positions anterior pair-rule stripes in the {{\em
                  {D}rosophila}} embryo},
  journal    = {Developmental Biology},
  year       = {2004},
  volume     = {276},
  pages      = {541-551}
}

@Article{Angulo03,
  author       = "J. Angulo and J. Serra",
  title        = "Automatic analysis of {DNA} microarray images using
                 mathematical morphology",
  journal      = "Bioinformatics",
  year         = "2003",
  volume       = "19",
  number       = "5",
  pages        = "553--562",
}

@Article{Aravin03,
  author       = "A. A. Aravin and M. Lagos-Quintana and A. Yalcin and
                 M. Zavolan and D. Marks and B. Snyder and T.
                 Gaasterland and J. Meyer and T. Tuschl",
  title        = "The Small {RNA} Profile during {{\em {D}rosophila
                 melanogaster}} Development",
  journal      = "Developmental Cell",
  year         = "2003",
  volume       = "5",
  pages        = "337--350",
}

@Article{Arias06,
  author       = "A. M. Arias and P. Hayward",
  title        = "Filtering transcriptional noise during development:
                  concepts and mechanisms",
  journal      = "Nature Reviews Genetics",
  year         = "2006",
  volume       = "7",
  pages        = "34--44",
}


@Article{Arkin98,
  author =   {Adam Arkin and John Ross and Harley H. MacAdams},
  title =    {Stochastic Kinetic Analysis of Developmental Pathway
                  Bifurcation in Phage $\lambda$-infected
                  {{\em {E}scherichia coli}} cells},
  journal =      {Genetics},
  year =     {1998},
  volume =   {149},
  pages =    {1633-1648}
}

@Article{Arnosti96b,
  author =   {D. N. Arnosti and S. Barolo and M. Levine and S. Small},
  title =    {The eve stripe 2 enhancer employs multiple modes of
                  transcriptional synergy},
  journal =      {Development},
  year =     {1996},
  volume =   {122},
  pages =    {205-214},
}



@Article{Artavanis91,
  author       = "S. Artavanis-Tsakonas and P. Simpson",
  title        = "Choosing a cell fate: a view from the {\em {N}otch}
                 locus",
  journal      = "Trends in Genetics",
  volume       = "7",
  year         = "1991",
  pages        = "403--408"
}


@Article{Ashyralyiev08,
  author       = "M. Ashyraliyev and J. Jaeger and J. G. Blom",
  title        = "Parameter estimation and determinability analysis
                  applied to {{\em {D}rosophila}} gap gene circuits",
  journal      = "BMC Systems Biology",
  year         = "2008",
  volume       = "2",
  pages        = "83",
}



@Article{Ashyralyiev09,
  author =   {M. Ashyraliyev and K. Siggens and H. Janssens and
                  J. Blom and M. Akam and J. Jaeger},
  title =    {Gene Circuit Analysis of the Terminal Gap Gene {\em huckebein}},
  journal =      {{PLOS} Computational Biology},
  year =     {2009},
  volume =   {5},
  pages =    {e1000548},
}

@Article{Audibert02,
  author       = "A. Audibert and D. Weil and F. Dautry",
  title        = "In vivo kinetics of mRNA splicing and transport in mammalian cells",
  journal      = "Molecular Cell Biol.",
  volume       = "22",
  year         = "2002",
  pages        = "6706--6718"
}


@InCollection{Azencott92,
  author =   "R. Azencott",
  title =    "Sequential simulated annealing: Speed of convergence
                  and acceleration techniques",
  booktitle =    "Simulated Annealing: Parallelization Techniques",
  year =     "1992",
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  pages        = "558--568",
}

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  year         = "2007",
  volume       = "315",
  pages        = "233--237",
}

@Article{Magde74,
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  journal    = {PLoS Computational Biology},
  year       = {2007},
  volume     = {3},
  pages      = {e130.doi:10.1371/journal.pcbi.0030130},
}

@Article{Mahoney87,
  author       = "P. A. Mahoney and J. A. Lengyel",
  title        = "The zygotic segmentation mutant {\em tailless} alters
                 the blastoderm fate map of the {{\em {D}rosophila}}
                 embryo",
  journal      = "Developmental Biology",
  year         = "1987",
  volume       = "122",
  pages        = "464--470",
}

@article{Maly02,
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                        the Saltatory Movement},
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        year    = {2002},
        volume  = {216},
        pages   = {59-71}
}

@Article{Manoukian92,
  author       = "A. S. Manoukian and H. M. Krause",
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  year         = "1992",
  volume       = "6",
  pages        = "1740--1751",
}

@PhdThesis{Manu07,
  author =   {Manu},
  title =    {Canalization of Gap Gene Expression During Early
              Development in {D}rosophila melanogaster},
  school =   {Stony Brook University},
  year =     {2007},
  type =     {{P}h{D} {T}hesis, {D}epartment of {A}pplied
              {M}athematics and {S}tatistics}
}

@Article{Manu09a,
    author = {Manu and S. Surkova and A. V. Spirov and
                V. Gursky and H. Janssens and A. Kim and O. Radulescu
                and C. E.  Vanario-Alonso and D. H. Sharp and
                M. Samsonova and J. Reinitz},
    title = {Canalization of gene expression in the
            {{\em {D}rosophila}} blastoderm by gap gene cross
            regulation},
        journal = {PLoS Biology},
    year = {2009},
        volume = {7},
        pages = {e1000049},
    note = {doi:10.371/journal.pbio.1000049},
}


@Article{Manu09b,
    author = {Manu and S. Surkova and A. V. Spirov and
                V. Gursky and H. Janssens and A. Kim and O. Radulescu
                and C. E.  Vanario-Alonso and D. H. Sharp and
                M. Samsonova and J. Reinitz},
    title = {Canalization of gene expression and domain shifts in the
            {{\em {D}rosophila}} blastoderm by dynamical attractors},
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        pages = {e1000303},
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}



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}

@InProceedings{Marnellos96,
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                 Algorithms in Biological Problems that Use Recurrent
                 Neural Nets",
  editor       = "G. W. Cottrell",
  pages        = "806",
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                 Cognitive Science Society",
  year         = "1996",
  publisher    = "Lawrence Erlbaum Associates",
}

@Article{MartinezArias85,
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  journal      = "Nature",
  year         = "1985",
  volume       = "313",
  pages        = "639--642",
}

@Article{MartinezArias88,
  author       = "A. Martinez-Arias and N. E. Baker and P. W. Ingham",
  title        = "Role of segment polarity genes in the definition and
                 maintenance of cell states in the {{\em {D}rosophila}}
                 embryo",
  journal      = "Development",
  year         = "1988",
  volume       = "103",
  pages        = "157--170",
}

@Article{Martins03,
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  number = {3},
  pages = {245--262},
}

@Article{Maurer80,
  author       = "R. Maurer and B. Meyer and M. Ptashne",
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                 negative control by repressor",
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  year         = "1980",
  volume       = "139",
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}

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  year         = "1982",
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}

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  year =     {1995},
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  pages =    {650-656}
}

@Misc{McCallion06,
  author =   {Andrew S. McCallion},
  title =    {{Faculty of 1000 {B}iology}},
  note =     { 25 Oct 2006 http://www.f1000biology.com/article/id/1047692/evaluation},
}

@article{McCarty03,
	title = "Selective Dimerization of a \{C2H2\} Zinc Finger Subfamily ",
	journal = "Molecular Cell ",
	volume = "11",
	number = "2",
	pages = "459 - 470",
	year = "2003",
	note = "",
	issn = "1097-2765",
	doi = "http://dx.doi.org/10.1016/S1097-2765(03)00043-1",
	url = "http://www.sciencedirect.com/science/article/pii/S1097276503000431",
	author = "Aaron S McCarty and Gary Kleiger and David Eisenberg and Stephen T Smale",
	abstract = "The \{C2H2\} zinc finger is the most prevalent protein motif in the mammalian proteome. Two \{C2H2\} fingers in Ikaros are dedicated to homotypic interactions between family members. We show here that these fingers comprise a bona fide dimerization domain. Dimerization is highly selective, however, as homologous domains from the TRPS-1 and Drosophila Hunchback proteins support homodimerization, but not heterodimerization with Ikaros. Ikaros-Hunchback selectivity is determined by 11 residues concentrated within the α-helical regions typically involved in base recognition. Preferential homodimerization of one chimeric protein predicts a parallel dimer interface and establishes the feasibility of creating novel dimer specificities. These results demonstrate that the \{C2H2\} motif provides a versatile platform for both sequence-specific protein-nucleic acid interactions and highly specific dimerization. "
}


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  year         = "1997",
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}

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}

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}

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}

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}


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}




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}

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}

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  title        = "Models of Biological Pattern Formation",
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  publisher    = "Academic Press",
  address      = "New York",
}

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                 Morphology",
  year         = "1983",
  volume       = "76",
  pages        = "115--137",
}

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                 Morphology",
  year         = "1983",
  volume       = "76",
  pages        = "139--146",
}

@Article{Meinhardt86,
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  year         = "1986",
  volume       = "4",
  pages        = "357--381",
}

@Article{Meinhardt88,
  author       = "H. Meinhardt",
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  year         = "1988",
  volume       = "104",
  pages        = "95--110",
}


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}

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                 Genetic Networks, With Examples From the Segment
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@Article{MeyerBJ80a,
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                 bacteriophage lambda. {II}. {OR}1, {OR}2, and {OR}3:
                 their roles in mediating the effects of repressor and
                 cro",
  journal      = "The Journal of Molecular Biology",
  year         = "1980",
  volume       = "139",
  pages        = "163--194",
}

@Article{MeyerBJ80b,
  author       = "B. J. Meyer and M. Ptashne",
  title        = "Gene regulation at the right operator ({OR}) of
                 bacteriophage lambda. {III}. lambda repressor directly
                 activates gene transcription",
  journal      = "The Journal of Molecular Biology",
  year         = "1980",
  volume       = "139",
  pages        = "195--205",
}

@Book{MeyerY93,
  author       = "Y. Meyer",
  title        = "Wavelets, algorithms and applications",
  year         = "1993",
  publisher    = "Siam, Philadelphia, USA",
}



@article{Minden89,
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   volume    = {109},
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@Article{Mjolsness89,
  author       = "E. Mjolsness and D. H. Sharp and B. K. Alpert",
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  year         = "1989",
  volume       = "10",
  pages        = "137--163",
}


@Article{Mjolsness91,
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  title        = "A connectionist model of development",
  journal      = "The Journal of Theoretical Biology",
  year         = "1991",
  volume       = "152",
  pages        = "429--453",
}

@InCollection{Mjolsness95,
  author       = "E. Mjolsness and C. D. Garrett and J. Reinitz and D.
                 H. Sharp",
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  chapter      = "7",
  year         = "1995",
  editor       = "W. Banzhaf and F. H. Eeckman",
  publisher    = "Springer Verlag",
  address      = "Berlin",
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}

@Article{Mlodzik85,
  author       = "M. Mlodzik and A. Fjose and W. J. Gehring",
  title        = "Isolation of {\em caudal}, a {{\em {D}rosophila}} homeo
                 box- containing gene with maternal expression, whose
                 transcripts form a concentration gradient at
                 pre-blastoderm stage",
  journal      = "The EMBO Journal",
  year         = "1985",
  volume       = "4",
  pages        = "2961--2969",
}

@Article{Mlodzik87a,
  author       = "M. Mlodzik and W. J. Gehring",
  title        = "Expression of the {\em caudal} gene in the germ line
                 of {{\em {D}rosophila}}: formation of an {RNA} and
                 protein gradient during early embryogenesis",
  journal      = "Cell",
  year         = "1987",
  volume       = "48",
  pages        = "465--478",
}

@Article{Mlodzik87b,
  author       = "M. Mlodzik and W. J. Gehring",
  title        = "Hierarchy of the genetic interactions that specify the
                 anteroposterior segmentation pattern of the {{\em
                 {D}rosophila}} embryo as monitored by {\em caudal}
                 protein expression",
  journal      = "Development",
  year         = "1987",
  volume       = "101",
  pages        = "421--435",
}

@Article{Mlodzik90,
  author       = "M. Mlodzik and G. Gibson and W. J. Gehring",
  title        = "Effects of ectopic expression of {\em caudal} during
                 {{\em {D}rosophila}} development",
  journal      = "Development",
  year         = "1990",
  volume       = "109",
  pages        = "271--277",
}


@Article{Mohler89,
  author       = "J. Mohler and E. D. Eldon and V. Pirrotta",
  title        = "A novel spatial transcription pattern associated with
                 the segmentation gene, {\em giant}, of {{\em
                 {D}rosophila}}",
  journal      = "The EMBO Journal",
  year         = "1989",
  volume       = "8",
  pages        = "1539--1548",
}

@BOOK{Molotkov88,
  author       = " I.A. Molotkov and S. Vakulenko",
  title        = "Sosredotochennye nelineinye volny (Russian)
               [Localized nonlinear waves]",
  publisher    ="Leningrad. Univ., Leningrad",
  year         = "1988",
  pages        ="240 pp",
}

@article{Monk03,
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   year      = {2003},
   volume    = {13},
   pages     = {1-20}
}

@Article{Morcillo97,
  author       = "P. Morcillo and C. Rosen and M. K. Baylies and D.
                 Dorsett",
  title        = "Chip, a widely expressed chromosomal protein required
                 for segmentation and activity of a remote wing margin
                 enhancer in {{\em {D}rosophila}}",
  journal      = "Genes and Development",
  year         = "1997",
  volume       = "11",
  pages        = "2729--2740",
}

@Article{Moreno99,
  author       = "E. Moreno and G. Morata",
  title        = "{\em caudal} is the hox gene that specifies the most
                 posterior {{\em {D}rosophila}} segment",
  journal      = "Nature",
  year         = "1999",
  volume       = "400",
  pages        = "873--877",
}

@Article{Morin01,
  author = {Xavier Morin and Richard Daneman and Michael Zavortink and William Chia},
  title = {A protein trap strategy to detect {GFP}-tagged proteins
                  expressed from their endogenous loci in {{\em {D}rosophila}}},
  journal = {Proceedings of the National Academy of Sciences USA},
  year = {2001},
  volume = {98},
  pages = {15050-15055},
}


@article{Morize98,
   author    = {P. Morize and A. E. Christiansen and M. Costa and
                  S. Parks and E. Wieschaus},
   title     = {Hyperactivation of the {\em folded gastrulation}
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   journal   = {Development},
   year      = {1998},
   volume    = {125},
   pages     = {589-597}
}


@article{Morozov09,
   author    = {A. V. Morozov and K. Fortney and D. A. Gaykalova and
                V. M. Studitsky and J. Widom and E. D. Siggia},
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   year      = {2009},
   volume    = {37},
   pages     = {4707-4722}
}

@Article{Mullen95,
  author       = "J. R. Mullen and S. DiNardo",
  title        = "Establishing parasegments in {{\em {D}rosophila}}
                 embryos: Roles of the {\em odd-skipped} and {\em naked}
                 genes",
  journal      = "Developmental Biology",
  year         = "1995",
  volume       = "169",
  pages        = "295--308",
}

@InProceedings{Muller32,
  author       = "H. J. Muller",
  title        = "Further Studies on the Nature and Causes of Gene
                 Mutations",
  booktitle    = "Sixth International Congress of Genetics",
  year         = "1932",
  pages        = "213--255",
  volume       = "1",
}

@article{Muller96,
   author    = {H. A. J. Muller and E. Wieschaus},
   title     = {{\em armadillo}, {\em bazooka}, and {\em stardust} are critical
               for early stages in formation of the zonula adherens and
               maintenance of the polarized blastoderm epithelium in {{\em {D}rosophila}}},
   journal   = {The Journal of Cell Biology},
   year      = {1996},
   volume    = {134},
   pages     = {149-163}
}

@Article{Murata95,
  author       = "Y. Murata and R. P. Wharton",
  title        = "Binding of {P}umilio to maternal {\em hunchback}
                 m{RNA} is required for posterior patterning in {{\em {D}rosophila}} embryos",
  journal      = "Cell",
  year         = "1995",
  volume       = "80",
  pages        = "747--756",
}

@Article{Muratov03,
  author       = "C. B. Muratov and S. Y. Shvartsman",
  title        = "An asymptotic study of the inductive pattern
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  year         = "2003",
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  pages        = "93--108",
}

@Book{Murray89,
  author       = "J. D. Murray",
  title        = "Mathematical Biology",
  year         = "1989",
  publisher    = "Springer, Berlin",
}

@Article{Myasnikova00a,
  author       = "E. Myasnikova and M. Samsonova and K. Kozlov and J.
                 Reinitz and D. Kosman",
  title        = "Method for spatial registration of the expression
                 patterns of {{\em {D}rosophila}} segmentation genes using
                 wavelets",
  journal      = "Computational Technologies",
  year         = "2000",
  volume       = "5",
  pages        = "112--119",
}

@InProceedings{Myasnikova00b,
  author       = "E. Myasnikova and A. Samsonova and M. Samsonova and J.
                 Reinitz",
  title        = "Spatial Registration of {\it in situ} Gene Expression
                 Data",
  booktitle    = "Computation in Cells: Proceedings of an EPSRC Emerging
                 Computing Paradigms Workshop",
  address      = "Univ. of Hertfordshire, UK",
  publisher    = "Dept. of Computer Science, Technical report No: 345",
  pages        = "21--26",
  year         = "2000",
}

@Article{Myasnikova01a,
  author =   {Ekaterina Myasnikova and Anastassia Samsonova and
                  Konstantin Kozlov and Maria Samsonova and John Reinitz},
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  volume       = "102",
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@article{Wright94,
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@Article{WuX98,
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@Article{WuY07,
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@article{Yiou96,
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@Article{Yu94,
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@Article{Yu95,
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@Article{Yu96,
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}

@Article{Yu97,
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  year         = "1997",
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@Article{YuD08,
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@Article{Yuan96,
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}

@Article{Yuan99,
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@Article{Yuh01,
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}


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@Article{Zinzen06,
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@Unpublished{Doedel07,
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% $Log: gul2.bib,v $
% Revision 1.34  2010/06/09 17:23:49  reinitz
% Added Deodel07 from Vitaly.
%
% Revision 1.33  2010/06/08 01:03:12  reinitz
% Discovered cleanup in last entry was incomplete at beinning of alphabet; fixed.
% Also added long comment at beinnin about lab conventions.
%
% Revision 1.32  2010/06/07 23:08:08  reinitz
% Added in new stuff, including last minute additions from 10/09 promoter
% grant, whatever I added my personal copy over the winter, and some new
% things for the 9/10 promoters proposal. Also went over whole files visually
% and made format repairs, checked for syntax with emacs bibtex-checker --JR.
%
% Revision 1.29  2009/10/05 04:42:50  reinitz
% Fixed vast number of capitalization errors (maybe incomplete, searched
% on 'melanogaster'), corrected
% typos in several entries, and added warning comment at the top.
% This file should be cleaned by hand, every entry inspected.
%
% Revision 1.28  2009/10/05 03:06:19  reinitz
% {\em {D}rosophila} --> {{\em {D}rosophila}} in 13 new entries.
%
% Revision 1.27  2009/10/05 00:26:21  cmartinez
%
% Fixed capitalization of new gul2.bib entries
%
% Revision 1.26  2009/10/04 21:31:54  reinitz
% Added Yves Fomekong-Nanfack thesis, Lisa thesis (cleaned up dup),
% and Masha's AD refs.
%
% Revision 1.25  2009/10/04 17:27:19  cmartinez
% Carlos:Latest gul2.bib update for promoters09j.tex
%
% Revision 1.24  2009/10/04 16:18:28  banwise
% Updated by Ah-Ram, but need to be updated more.
%
% Revision 1.23  2009/10/04 09:34:27  cmartinez
% Carlos: added unresolved references for promoters09i.tex
%
% Revision 1.22  2009/10/03 20:22:25  reinitz
% Updated refs for grant by JR.
%
% Revision 1.21  2009/10/03 15:03:12  cmartinez
% Carlos: fixed LawrenceCE90 reference
%
% Revision 1.20  2009/10/03 14:47:27  cmartinez
% Updated gul2.bib with references for transcription grant
%
% Revision 1.19  2009/10/02 07:58:29  cmartinez
% Carlos: Added new references for Aim 4 of promoters09 grant
%
% Revision 1.18  2009/07/03 15:19:07  reinitz
% Added Carlos' 09 refs from Cmartinez.bib
%
% Revision 1.17  2009/07/02 19:56:07  reinitz
% Added keywords and log.
%


@String{revmp = {Rev. Mod. Phys.}}

@Book{Jeffreys:1929,
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@Book{Reiner:1965,
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@Book{Rice:1985,
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@Article{Mischenko12,
  author = 	 {\C5.\CB. \CC\E8\F9\E5\ED\EA\EE and \CD.\C2. \C8\E2\E0\ED\E8\F1\E5\ED\EA\EE and \C8.\D0. \C0\EA\E1\E5\F0\E4\E8\ED and \CF.\D1. \C4\E5\EC\E5\ED\EA\EE\E2 and \C2.\C0. \CB\E8\F5\EE\F8\E2\E0\E9 and \CD.\C0. \CA\EE\EB\F7\E0\ED\EE\E2 and \C2.\C0. \C8\E2\E0\ED\E8\F1\E5\ED\EA\EE},
  title = 	 {\CF\EE\E4\E0\E2\EB\E5\ED\E8\E5 \F0\E5\EF\EB\E8\EA\E0\F6\E8\E8 \F1\F3\E1\E3\E5\ED\EE\EC\ED\EE\E3\EE \D0\CD\CA \F0\E5\EF\EB\E8\EA\EE\ED\E0 \E2\E8\F0\F3\F1\E0 \E3\E5\EF\E0\F2\E8\F2\E0 \F1 \E8\ED\E3\E8\E1\E8\F2\EE\F0\EE\EC NS3 \EF\F0\EE\F2\E5\E0\E7\FB sch 503034 \E2 huh-7 \EA\EB\E5\F2\EA\E0\F5: \F1\F2\EE\F5\E0\F1\F2\E8\F7\E5\F1\EA\E0\FF \EC\EE\E4\E5\EB\FC},
  journal = 	 {\C2\E0\E2\E8\EB\EE\E2\F1\EA\E8\E9 \E6\F3\F0\ED\E0\EB \E3\E5\ED\E5\F2\E8\EA\E8 \E8 \F1\E5\EB\E5\EA\F6\E8\E8},
  year = 	 {2012},
  volume =	 {16},
  number = {2},
  pages =	 {339--347}
}

@Article{Ivanisenko13,
  author = 	 {\C8\E2\E0\ED\E8\F1\E5\ED\EA\EE \CD.\C2. and \CC\E8\F9\E5\ED\EA\EE \C5.\CB. and \C0\EA\E1\E5\F0\E4\E8\ED \C8.\D0. and \C4\E5\EC\E5\ED\EA\EE\E2 \CF.\D1. and \CB\E8\F5\EE\F8\E2\E0\E9 \C2.\C0. and \CA\EE\E7\EB\EE\E2 \CA.\CD and \D2\EE\E4\EE\F0\EE\E2 \C4. and \D1\E0\EC\F1\EE\ED\EE\E2\E0 \CC.\C3. and \D1\E0\EC\F1\EE\ED\EE\E2 \C0.\CC. and \CA\EE\EB\F7\E0\ED\EE\E2 \CD.\C0. and \C8\E2\E0\ED\E8\F1\E5\ED\EA\EE \C2.\C0.},
  title = 	 {\D0\E5\EF\EB\E8\EA\E0\F6\E8\FF \F1\F3\E1\E3\E5\ED\EE\EC\ED\EE\E3\EE \F0\E5\EF\EB\E8\EA\EE\ED\E0 \E2\E8\F0\F3\F1\E0 \E3\E5\EF\E0\F2\E8\F2\E0 \D1 \E2 \EF\F0\E8\F1\F3\F2\F1\F2\E2\E8\E8 \E8\ED\E3\E8\E1\E8\F2\EE\F0\EE\E2 NS3 \EF\F0\EE\F2\E5\E0\E7\FB: c\F2\EE\F5\E0\F1\F2\E8\F7\E5\F1\EA\E0\FF \EC\EE\E4\E5\EB\FC},
  journal = 	 {\CC\E0\F2\E5\EC\E0\F2\E8\F7\E5\F1\EA\E0\FF \E1\E8\EE\EB\EE\E3\E8\FF \E8 \E1\E8\EE\E8\ED\F4\EE\F0\EC\E0\F2\E8\EA\E0},
  year = 	 {2013},
  volume =	 {\EF\F0\E8\ED\FF\F2\E0 \E2 \EF\E5\F7\E0\F2\FC}
}

@Article{Pisarev13,
  author = 	 {\C0.C. \CF\E8c\E0p\E5\E2 and \CC.\C3. C\E0\ECc\EE\ED\EE\E2\E0},
  title = 	 {\CC\E5\F2\EE\E4 p\E5\F8\E5\ED\E8\FF \EC\ED\EE\E3\EE\EAp\E8\F2\E5p\E8\E0\EB\FC\ED\FBx \EE\E1p\E0\F2\ED\FBx \E7\E0\E4\E0\F7 \E2 \F3c\EB\EE\E2\E8\FFx \ED\E5\EE\EFp\E5\E4\E5\EB\E5\ED\ED\EEc\F2\E8},
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	doi       = {10.1137/0906002}
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@Book{Petukhov82,
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@Article{Ioffe52,
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@MISC{Fowlkes08,
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@article{Little11,
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volume = {9},
year = {2011}
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@Article{Papatsenko11,
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@article{vonDassow02,
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   year      = {2002},
   volume    = {294},
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@article{Hu07,
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@article{Wunderlich09,
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   number    = {10},
   pages     = {434--440}
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@article{Biggin11,
   author    = {Biggin, Mark D},
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   volume    = {21},
   number    = {4},
   pages     = {611--626}
}

@Book{Bates88,
	Author  = {Douglas M. Bates and Donald G. Watts},
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	Title     = {Nonlinear Regression Analysis and Its Applications},
	Year      = {1988}
}

@article{Brun01,
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   year      = {2001},
   volume    = {37},
   number    = {4},
   doi = {10.1029/2000WR900350},
   annotation = {Large environmental simulation models are usually overparameterized with respect to given sets of observations. This results in poorly identifiable or nonidentifiable model parameters. For small models, plots of sensitivity functions have proven to be useful for the analysis of parameter identifiability. For models with many parameters, however, near-linear dependence of sensitivity functions can no longer be assessed graphically. In this paper a systematic approach for tackling the parameter identifiability problem of large models based on local sensitivity analysis is presented. The calculation of two identifiability measures that are easy to handle and interpret is suggested. The first accounts for the sensitivity of model results to single parameters, and the second accounts for the degree of near-linear dependence of sensitivity functions of parameter subsets. It is shown how these measures provide identifiability diagnosis for parameter subsets, how they are able to guide the selection of identifiable parameter subsets for parameter estimation, and how they facilitate the interpretation of the correlation matrix of the parameter estimate with respect to parameter identifiability. In addition, we show how potential bias of the parameter estimates, due to a priori fixing of some of the parameters, can be analyzed. Finally, two case studies are presented in order to illustrate the suggested approach.},
   pages     = {1015--1030}
}


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%34 16940091
@Article{pmid16940091,
   Author="Ma, S.  and Boerner, J. E.  and TiongYip, C.  and Weidmann, B.  and Ryder, N. S.  and Cooreman, M. P.  and Lin, K. ",
   Title="{{N}{I}{M}811, a cyclophilin inhibitor, exhibits potent in vitro activity against hepatitis {C} virus alone or in combination with alpha interferon}",
   Journal="Antimicrob. Agents Chemother.",
   Year="2006",
   Volume="50",
   Number="9",
   Pages="2976--2982",
   Month="Sep"
}

% 17045684
@Article{Ananiadou:2006,
   Author="Ananiadou, S.  and Kell, D. B.  and Tsujii, J. ",
   Title="{{T}ext mining and its potential applications in systems biology}",
   Journal="Trends Biotechnol.",
   Year="2006",
   Volume="24",
   Number="12",
   Pages="571--579",
   Month="Dec"
}

@article{Seiwert08,
    abstract = {Future treatments for chronic {HCV} infection are likely to include agents that target viral components directly. Here, the preclinical characteristics of {ITMN}-191, a peptidomimetic inhibitor of the {NS3}/{4A} protease of {HCV}, are described. {ITMN}-191 inhibited a reference genotype 1 {NS3}/{4A} protein in a time dependent fashion; a hallmark of an inhibitor with a two-step binding mechanism and a slow dissociation rate. Under pre-equilibrium conditions 290 {pM} {ITMN}-191 half-maximally inhibited the reference {NS3}/{4A} protease, but a 35,000-fold higher concentration did not appreciably inhibit a panel of 79 proteases, ion channels, transporters and cell surface receptors. Sub-nanomolar biochemical potency was maintained against {NS3}/{4A} derived from {HCV} genotypes 4, 5 and 6, while single-digit nanomolar potency was observed against {NS3}/{4A} from genotypes 2b and 3a. Dilution of preformed enzyme inhibitor complex indicated {ITMN}-191 remained bound to and inhibited {NS3}/{4A} for more than 5 hours after its initial association. In cell-based potency assays, half-maximal reduction of genotype 1b {HCV} replicon {RNA} was afforded by 1.8 {nM}; 45 {nM} eliminated {HCV} replicon from cells. Peginterferon alfa-2a displayed a significant degree of antiviral synergy with {ITMN}-191 and reduced the concentration of {ITMN}-191 required for {HCV} replicon elimination. A 30 mg/kg oral dose administered to rat or monkey yielded liver concentrations 12 hours after dosing that exceeded the {ITMN}-191 concentration required to eliminate replicon {RNA} from cells. These preclinical characteristics compare favorably to other inhibitors of {NS3}/{4A} in clinical development and therefore support the clinical investigation of {ITMN}-191 for the treatment of chronic hepatitis C. {10.1128/AAC}.00699-08},
    author = {Seiwert, Scott D. and Andrews, Steven W. and Jiang, Yutong and Serebryany, Vladimir and Tan, Hua and Kossen, Karl and Rajagopalan, Ravi P. T. and Misialek, Shawn and Stevens, Sarah K. and Stoycheva, Antitsa and Hong, Jin and Lim, Sharlene R. and Qin, Xiaoli and Rieger, Robert and Condroski, Kevin R. and Zhang, Hailong and Do, Mary G. and Lemieux, Christine and Hingorani, Gary P. and Hartley, Dylan P. and Josey, John A. and Pan, Lin and Beigelman, Leonid and Blatt, Lawrence M.},
    citeulike-article-id = {3359441},
    citeulike-linkout-0 = {http://dx.doi.org/10.1128/aac.00699-08},
    citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18824605},
    citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18824605},
    day = {29},
    doi = {10.1128/aac.00699-08},
    journal = {Antimicrob. Agents Chemother.},
    keywords = {hcv, itmn-191},
    month = "sep",
    pages = {AAC.00699-08+},
    pmid = {18824605},
    posted-at = {2008-09-30 16:32:57},
    priority = {2},
    title = {Preclinical characteristics of the {HCV} {NS3}/{4A} protease inhibitor {ITMN}-191 (R7227)},
    url = {http://dx.doi.org/10.1128/aac.00699-08},
    year = {2008}
}

@article{Mathy08,
    author = {Joanna E. Mathy and Sue Ma and Teresa Compton and Kai Lin},
    title = {Combinations of Cyclophilin Inhibitor NIM811 with Hepatitis C Virus NS3-4A Protease or NS5B Polymerase Inhibitors Enhance Antiviral Activity and Suppress the Emergence of Resistance},
    journal = {Antimicrob Agents Chemother},
    year = {2008},
    month = {September},
    volume = {52},
    number = {9}, 
    pages = {3267--3275}
}

@article{Coelmont09,
    author = {Coelmont L and Kaptein S and Paeshuyse J and Vliegen I and Dumont JM and Vuagniaux G and Neyts J.},
    title = {Debio 025, a cyclophilin binding molecule, is highly efficient in clearing hepatitis C virus (HCV) replicon-containing cells when used alone or in combination with specifically targeted antiviral therapy for HCV (STAT-C) inhibitors.},
    journal = {Antimicrob Agents Chemother},
    year = {2009},
    month = {March},
    volume = {53},
    number = {3}, 
    pages = {967--976}
}


@TechReport{Liang14,
  author = {J. J. Liang and B. Y. Qu and P. N. Suganthan},
  title = {Problem Definitions and Evaluation Criteria for the CEC 2014 Special Session and Competition on Single Objective Real-Parameter Numerical Optimization},
  institution = {Computational Intelligence Laboratory, Zhengzhou University, Zhengzhou China And Technical Report, Nanyang Technological University, Singapore},
  year = {2014},
  number = {Technical Report 201311}
}

@Article{Erlich14,
  author       = "Istvan Erlich and Jose L. Rueda and Sebastian Wildenhues",
  title        = "Evaluating the Mean-Variance Mapping Optimization on the IEEE-CEC 2014 Test Suite",
  journal      = "CEC 2014 Special Session and Competition on Single Objective Real-Parameter Numerical Optimization",
  year         = "2014"
}

@Article{Tanabe14,
  author       = "Ryoji Tanabe and Alex S. Fukunaga",
  title        = "Improving The Search Performance of SHADE By Using Linear Population Size Reduction",
  journal      = "CEC 2014 Special Session and Competition on Single Objective Real-Parameter Numerical Optimization",
  year         = "2014"
}

@Article{Elsayed14,
  author       = "Saber M. Elsayed and Ruhul A. Sarker and Daryl L. Essam and Noha M. Hamza",
  title        = "Testing United Multi-Operator Evolutionary Algorithms on The CEC2014 Real-Parameter Numerical Optimization",
  journal      = "CEC 2014 Special Session and Competition on Single Objective Real-Parameter Numerical Optimization",
  year         = "2014"
}

@Article{Chen14,
  author       = "Lei Chen and Hai-Lin Liu and Zhe Zheng and Shengli Xie",
  title        = "A Evolutionary Algorithm Based on Covariance Matrix Leaning and Searching Preference for Solving CEC 2014 Benchmark Problems",
  journal      = "CEC 2014 Special Session and Competition on Single Objective Real-Parameter Numerical Optimization",
  year         = "2014"
}

@Article{Yashesh14,
  author       = "Dhebar Yashesh and Kalyanmoy Deb and Sunith Bandaru",
  title        = "Non-Uniform Mapping in Real-Coded Genetic Algorithms",
  journal      = "CEC 2014 Special Session and Competition on Single Objective Real-Parameter Numerical Optimization",
  year         = "2014"
}
